Starting phenix.real_space_refine on Sat Jun 6 11:02:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9frj_50715/06_2026/9frj_50715.cif Found real_map, /net/cci-nas-00/data/ceres_data/9frj_50715/06_2026/9frj_50715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9frj_50715/06_2026/9frj_50715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9frj_50715/06_2026/9frj_50715.map" model { file = "/net/cci-nas-00/data/ceres_data/9frj_50715/06_2026/9frj_50715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9frj_50715/06_2026/9frj_50715.cif" } resolution = 2.66 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= 0.001 sd= 0.014 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 2 6.06 5 P 82 5.49 5 Mg 5 5.21 5 S 70 5.16 5 C 17198 2.51 5 N 4902 2.21 5 O 5320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27579 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1792 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 213} Chain: "B" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1797 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 214} Chain: "C" Number of atoms: 8628 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1091, 8606 Classifications: {'peptide': 1091} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1020} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1091, 8606 Classifications: {'peptide': 1091} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1020} Chain breaks: 2 bond proxies already assigned to first conformer: 8745 Chain: "D" Number of atoms: 10848 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1360, 10733 Classifications: {'peptide': 1360} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1291} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1367, 10787 Classifications: {'peptide': 1367} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1298} Chain breaks: 2 bond proxies already assigned to first conformer: 10853 Chain: "E" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 761 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 6, 'TRANS': 87} Chain: "F" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2147 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Chain: "G" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 696 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain breaks: 1 Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 792 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 6, 34 Unusual residues: {' MG': 3, ' ZN': 2, '2TM': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 82 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 2, 82 Unusual residues: {'2TM': 1, 'B4P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20062 SG CYS D1112 105.049 85.456 87.199 1.00 37.79 S ATOM 20706 SG CYS D1194 101.596 85.265 85.685 1.00 33.17 S ATOM 20762 SG CYS D1201 104.658 83.563 84.012 1.00 32.72 S ATOM 20786 SG CYS D1204 103.191 82.070 87.071 1.00 36.48 S ATOM 12686 SG CYS D 58 73.319 124.777 43.901 1.00 99.43 S ATOM 12697 SG CYS D 60 70.274 127.158 43.256 1.00 98.84 S ATOM 12808 SG CYS D 73 73.283 128.241 45.681 1.00 95.65 S Residues with excluded nonbonded symmetry interactions: 19 residue: pdb=" N AARG C 345 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 345 " occ=0.50 residue: pdb=" N AARG C 802 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 802 " occ=0.50 residue: pdb=" N AARG D 586 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 586 " occ=0.50 residue: pdb=" N AARG D 674 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 674 " occ=0.50 residue: pdb=" N ATHR D1234 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR D1234 " occ=0.50 residue: pdb=" N AGLN D1235 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN D1235 " occ=0.50 residue: pdb=" N ALEU D1236 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU D1236 " occ=0.50 residue: pdb=" N ATHR D1237 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR D1237 " occ=0.50 residue: pdb=" N AMET D1238 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET D1238 " occ=0.50 residue: pdb=" N BARG D1239 " occ=0.50 ... (9 atoms not shown) pdb=" NH2BARG D1239 " occ=0.50 residue: pdb=" N BTHR D1240 " occ=0.50 ... (5 atoms not shown) pdb=" CG2BTHR D1240 " occ=0.50 residue: pdb=" N BPHE D1241 " occ=0.50 ... (9 atoms not shown) pdb=" CZ BPHE D1241 " occ=0.50 ... (remaining 7 not shown) Time building chain proxies: 9.21, per 1000 atoms: 0.33 Number of scatterers: 27579 At special positions: 0 Unit cell: (142.546, 171.722, 132.542, 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 2 29.99 S 70 16.00 P 82 15.00 Mg 5 11.99 O 5320 8.00 N 4902 7.00 C 17198 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: 2.20 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1204 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1201 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1194 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1112 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 58 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 73 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 60 " Number of angles added : 6 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6080 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 51 sheets defined 43.4% alpha, 18.9% beta 25 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.595A pdb=" N THR A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 152 through 157 removed outlier: 3.625A pdb=" N HIS A 156 " --> pdb=" O PRO A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 224 removed outlier: 3.647A pdb=" N TYR A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'B' and resid 31 through 47 Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 74 through 83 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.816A pdb=" N HIS B 156 " --> pdb=" O PRO B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 223 Processing helix chain 'C' and resid 19 through 31 removed outlier: 4.128A pdb=" N SER C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 removed outlier: 3.534A pdb=" N ARG C 39 " --> pdb=" O PRO C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 52 Processing helix chain 'C' and resid 79 through 86 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 215 through 222 removed outlier: 4.304A pdb=" N GLN C 219 " --> pdb=" O GLY C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 229 removed outlier: 3.706A pdb=" N MET C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 243 Processing helix chain 'C' and resid 249 through 262 Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 302 through 315 Processing helix chain 'C' and resid 335 through 362 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 375 through 389 Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 424 through 429 removed outlier: 3.614A pdb=" N ARG C 428 " --> pdb=" O GLY C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 435 removed outlier: 3.506A pdb=" N TYR C 435 " --> pdb=" O ARG C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 525 through 529 Processing helix chain 'C' and resid 535 through 540 Processing helix chain 'C' and resid 543 through 547 Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 554 through 565 Processing helix chain 'C' and resid 566 through 568 No H-bonds generated for 'chain 'C' and resid 566 through 568' Processing helix chain 'C' and resid 583 through 591 Processing helix chain 'C' and resid 683 through 687 removed outlier: 4.133A pdb=" N ASP C 686 " --> pdb=" O ASN C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 697 Processing helix chain 'C' and resid 730 through 734 Processing helix chain 'C' and resid 854 through 858 Processing helix chain 'C' and resid 872 through 874 No H-bonds generated for 'chain 'C' and resid 872 through 874' Processing helix chain 'C' and resid 875 through 880 removed outlier: 3.959A pdb=" N ARG C 879 " --> pdb=" O GLY C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 898 Processing helix chain 'C' and resid 910 through 933 removed outlier: 3.956A pdb=" N ARG C 929 " --> pdb=" O TYR C 925 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU C 932 " --> pdb=" O LYS C 928 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 950 Processing helix chain 'C' and resid 958 through 969 Processing helix chain 'C' and resid 1000 through 1004 Processing helix chain 'C' and resid 1033 through 1044 Processing helix chain 'C' and resid 1045 through 1054 Processing helix chain 'C' and resid 1059 through 1073 Processing helix chain 'C' and resid 1082 through 1095 removed outlier: 3.682A pdb=" N ARG C1086 " --> pdb=" O PRO C1082 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C1095 " --> pdb=" O GLU C1091 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.644A pdb=" N ASP D 107 " --> pdb=" O TRP D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 117 Processing helix chain 'D' and resid 119 through 128 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 372 through 376 Processing helix chain 'D' and resid 423 through 426 Processing helix chain 'D' and resid 457 through 468 Processing helix chain 'D' and resid 469 through 481 Processing helix chain 'D' and resid 485 through 506 removed outlier: 3.650A pdb=" N VAL D 498 " --> pdb=" O LYS D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 511 Processing helix chain 'D' and resid 521 through 525 Processing helix chain 'D' and resid 538 through 560 removed outlier: 3.989A pdb=" N ASP D 542 " --> pdb=" O SER D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 583 Processing helix chain 'D' and resid 602 through 608 Processing helix chain 'D' and resid 612 through 618 Processing helix chain 'D' and resid 646 through 653 Processing helix chain 'D' and resid 653 through 664 Processing helix chain 'D' and resid 669 through 679 removed outlier: 3.852A pdb=" N ARG D 679 " --> pdb=" O ARG D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 683 Processing helix chain 'D' and resid 685 through 695 removed outlier: 3.707A pdb=" N ASP D 689 " --> pdb=" O ASP D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 711 No H-bonds generated for 'chain 'D' and resid 709 through 711' Processing helix chain 'D' and resid 729 through 731 No H-bonds generated for 'chain 'D' and resid 729 through 731' Processing helix chain 'D' and resid 732 through 737 Processing helix chain 'D' and resid 752 through 762 Processing helix chain 'D' and resid 764 through 768 Processing helix chain 'D' and resid 783 through 794 Processing helix chain 'D' and resid 808 through 819 removed outlier: 3.525A pdb=" N ALA D 812 " --> pdb=" O THR D 808 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 841 removed outlier: 3.564A pdb=" N LEU D 839 " --> pdb=" O SER D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 855 Processing helix chain 'D' and resid 876 through 891 Processing helix chain 'D' and resid 892 through 900 Processing helix chain 'D' and resid 907 through 923 Processing helix chain 'D' and resid 923 through 945 removed outlier: 3.582A pdb=" N THR D 944 " --> pdb=" O THR D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 954 removed outlier: 3.576A pdb=" N ALA D 954 " --> pdb=" O ILE D 951 " (cutoff:3.500A) Processing helix chain 'D' and resid 958 through 980 removed outlier: 3.929A pdb=" N GLN D 962 " --> pdb=" O GLU D 958 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 972 " --> pdb=" O ASP D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 984 through 1015 Processing helix chain 'D' and resid 1018 through 1026 Processing helix chain 'D' and resid 1031 through 1040 Processing helix chain 'D' and resid 1066 through 1103 removed outlier: 3.786A pdb=" N HIS D1075 " --> pdb=" O PHE D1071 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY D1076 " --> pdb=" O ILE D1072 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA D1089 " --> pdb=" O ALA D1085 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP D1090 " --> pdb=" O LEU D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1136 through 1145 Processing helix chain 'D' and resid 1167 through 1180 Processing helix chain 'D' and resid 1190 through 1194 Processing helix chain 'D' and resid 1202 through 1206 Processing helix chain 'D' and resid 1220 through 1236 Proline residue: D1232 - end of helix removed outlier: 4.126A pdb=" N AGLN D1235 " --> pdb=" O GLU D1231 " (cutoff:3.500A) Processing helix chain 'D' and resid 1255 through 1264 Processing helix chain 'D' and resid 1331 through 1339 Processing helix chain 'D' and resid 1340 through 1360 removed outlier: 3.686A pdb=" N VAL D1355 " --> pdb=" O GLU D1351 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR D1356 " --> pdb=" O ILE D1352 " (cutoff:3.500A) Processing helix chain 'D' and resid 1364 through 1376 removed outlier: 4.492A pdb=" N ILE D1368 " --> pdb=" O HIS D1364 " (cutoff:3.500A) Processing helix chain 'D' and resid 1397 through 1411 Processing helix chain 'D' and resid 1423 through 1430 Processing helix chain 'D' and resid 1433 through 1441 Processing helix chain 'D' and resid 1442 through 1454 Processing helix chain 'D' and resid 1461 through 1468 removed outlier: 4.054A pdb=" N ASN D1465 " --> pdb=" O GLY D1461 " (cutoff:3.500A) Processing helix chain 'D' and resid 1474 through 1478 Processing helix chain 'D' and resid 1489 through 1500 Processing helix chain 'E' and resid 5 through 13 removed outlier: 3.735A pdb=" N VAL E 13 " --> pdb=" O LEU E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 33 Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.565A pdb=" N TRP E 63 " --> pdb=" O ASN E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 93 Processing helix chain 'F' and resid 79 through 90 removed outlier: 3.568A pdb=" N GLN F 83 " --> pdb=" O ASP F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 121 Processing helix chain 'F' and resid 123 through 137 Processing helix chain 'F' and resid 152 through 164 Processing helix chain 'F' and resid 170 through 200 removed outlier: 3.531A pdb=" N LEU F 174 " --> pdb=" O HIS F 170 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ARG F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL F 195 " --> pdb=" O ASN F 191 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL F 196 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 227 Processing helix chain 'F' and resid 228 through 232 removed outlier: 3.803A pdb=" N ARG F 231 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 255 removed outlier: 3.928A pdb=" N TYR F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TRP F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TRP F 242 " --> pdb=" O TYR F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 283 Processing helix chain 'F' and resid 287 through 296 removed outlier: 3.666A pdb=" N GLY F 296 " --> pdb=" O ALA F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 311 Processing helix chain 'F' and resid 330 through 333 removed outlier: 3.517A pdb=" N ILE F 333 " --> pdb=" O GLY F 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 330 through 333' Processing helix chain 'F' and resid 340 through 352 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 16 removed outlier: 6.447A pdb=" N ASP A 193 " --> pdb=" O PRO A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 104 removed outlier: 7.189A pdb=" N ASN A 139 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE A 58 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLU A 141 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL A 56 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARG A 143 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 107 through 110 Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AA6, first strand: chain 'A' and resid 229 through 230 removed outlier: 3.648A pdb=" N VAL B 13 " --> pdb=" O GLN A 229 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N TYR B 20 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR B 201 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLU B 22 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE B 199 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL B 24 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU B 197 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU B 26 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU B 195 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N THR B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU B 186 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 104 removed outlier: 7.495A pdb=" N ASN B 139 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE B 58 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLU B 141 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL B 56 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG B 143 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 89 Processing sheet with id=AA9, first strand: chain 'B' and resid 107 through 110 Processing sheet with id=AB1, first strand: chain 'B' and resid 150 through 151 Processing sheet with id=AB2, first strand: chain 'C' and resid 2 through 5 Processing sheet with id=AB3, first strand: chain 'C' and resid 65 through 73 removed outlier: 6.835A pdb=" N ARG C 97 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR C 71 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TYR C 95 " --> pdb=" O TYR C 71 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU C 73 " --> pdb=" O PRO C 93 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA C 92 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N HIS C 117 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU C 94 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AB5, first strand: chain 'C' and resid 331 through 334 removed outlier: 6.356A pdb=" N SER C 138 " --> pdb=" O SER C 411 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 145 through 150 removed outlier: 6.823A pdb=" N TYR C 158 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL C 176 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP C 173 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 186 " --> pdb=" O ARG C 189 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 291 through 294 Processing sheet with id=AB8, first strand: chain 'C' and resid 460 through 461 removed outlier: 5.548A pdb=" N GLU C 482 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N VAL C 475 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR C 480 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 460 through 461 Processing sheet with id=AC1, first strand: chain 'C' and resid 503 through 504 Processing sheet with id=AC2, first strand: chain 'C' and resid 595 through 596 removed outlier: 6.576A pdb=" N LEU C 595 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 620 through 624 removed outlier: 6.591A pdb=" N ARG C 610 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL C 606 " --> pdb=" O ARG C 610 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL C 612 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 629 through 630 Processing sheet with id=AC5, first strand: chain 'C' and resid 661 through 662 Processing sheet with id=AC6, first strand: chain 'C' and resid 971 through 972 removed outlier: 7.134A pdb=" N ILE C 688 " --> pdb=" O ALA C 850 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE C 852 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE C 690 " --> pdb=" O ILE C 852 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 689 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N VAL C 869 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU C 673 " --> pdb=" O VAL C 869 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU C 871 " --> pdb=" O LEU C 673 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA C 675 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL C 988 " --> pdb=" O ILE C 676 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 702 through 713 removed outlier: 8.237A pdb=" N ARG C 820 " --> pdb=" O ARG C 807 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ARG C 807 " --> pdb=" O ARG C 820 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL C 822 " --> pdb=" O ARG C 805 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ARG C 805 " --> pdb=" O VAL C 822 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG C 824 " --> pdb=" O THR C 803 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR C 803 " --> pdb=" O ARG C 824 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TYR C 826 " --> pdb=" O VAL C 801 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 721 through 722 Processing sheet with id=AC9, first strand: chain 'C' and resid 754 through 756 removed outlier: 6.772A pdb=" N LEU C 790 " --> pdb=" O LEU C 755 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1006 through 1008 removed outlier: 6.370A pdb=" N CYS D 642 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL D 721 " --> pdb=" O CYS D 642 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU D 644 " --> pdb=" O VAL D 721 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1031 through 1032 Processing sheet with id=AD3, first strand: chain 'C' and resid 1108 through 1109 removed outlier: 4.492A pdb=" N THR C1101 " --> pdb=" O VAL C1109 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 91 through 100 removed outlier: 10.167A pdb=" N LEU D 95 " --> pdb=" O PRO D 518 " (cutoff:3.500A) removed outlier: 10.961A pdb=" N THR D 97 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ALA D 516 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 152 through 153 removed outlier: 6.729A pdb=" N ASP D 453 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AD7, first strand: chain 'D' and resid 166 through 170 removed outlier: 6.980A pdb=" N VAL D 385 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL D 213 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU D 387 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL D 211 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLU D 389 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE D 207 " --> pdb=" O ALA D 391 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE D 393 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR D 205 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL D 395 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA D 203 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 184 through 185 removed outlier: 6.770A pdb=" N ALA D 203 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL D 395 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR D 205 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE D 393 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE D 207 " --> pdb=" O ALA D 391 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLU D 389 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL D 211 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU D 387 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL D 213 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL D 385 " --> pdb=" O VAL D 213 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 190 through 192 Processing sheet with id=AE1, first strand: chain 'D' and resid 352 through 353 removed outlier: 6.822A pdb=" N VAL D 377 " --> pdb=" O ILE D 367 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 398 through 402 removed outlier: 3.815A pdb=" N ASP D 413 " --> pdb=" O VAL D 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 420 through 422 removed outlier: 7.475A pdb=" N VAL D 427 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 527 through 529 Processing sheet with id=AE5, first strand: chain 'D' and resid 805 through 806 Processing sheet with id=AE6, first strand: chain 'D' and resid 842 through 843 Processing sheet with id=AE7, first strand: chain 'D' and resid 1106 through 1109 Processing sheet with id=AE8, first strand: chain 'D' and resid 1118 through 1121 Processing sheet with id=AE9, first strand: chain 'D' and resid 1123 through 1125 Processing sheet with id=AF1, first strand: chain 'D' and resid 1153 through 1155 Processing sheet with id=AF2, first strand: chain 'D' and resid 1300 through 1304 removed outlier: 3.580A pdb=" N GLY D1279 " --> pdb=" O VAL D1319 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D1319 " --> pdb=" O GLY D1279 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1394 through 1396 removed outlier: 5.494A pdb=" N VAL D1381 " --> pdb=" O LYS D1418 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS D1418 " --> pdb=" O VAL D1381 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1484 through 1488 Processing sheet with id=AF5, first strand: chain 'E' and resid 47 through 49 Processing sheet with id=AF6, first strand: chain 'F' and resid 320 through 321 removed outlier: 4.120A pdb=" N SER F 327 " --> pdb=" O ILE F 321 " (cutoff:3.500A) 1228 hydrogen bonds defined for protein. 3401 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 63 hydrogen bonds 126 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 7.44 Time building geometry restraints manager: 2.95 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: 8423 1.34 - 1.46: 4607 1.46 - 1.58: 14910 1.58 - 1.70: 155 1.70 - 1.82: 131 Bond restraints: 28226 Sorted by residual: bond pdb=" O3BB2TM D2006 " pdb=" PG B2TM D2006 " ideal model delta sigma weight residual 1.700 1.621 0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" O3BA2TM G2102 " pdb=" PG A2TM G2102 " ideal model delta sigma weight residual 1.700 1.629 0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" O5EAB4P G2101 " pdb=" PA AB4P G2101 " ideal model delta sigma weight residual 1.656 1.593 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" C THR C 715 " pdb=" N LYS C 716 " ideal model delta sigma weight residual 1.335 1.296 0.039 1.34e-02 5.57e+03 8.64e+00 bond pdb=" O5FAB4P G2101 " pdb=" PD AB4P G2101 " ideal model delta sigma weight residual 1.650 1.591 0.059 2.00e-02 2.50e+03 8.57e+00 ... (remaining 28221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 38166 2.89 - 5.78: 321 5.78 - 8.67: 27 8.67 - 11.56: 7 11.56 - 14.45: 2 Bond angle restraints: 38523 Sorted by residual: angle pdb=" PB A2TM G2102 " pdb=" O3BA2TM G2102 " pdb=" PG A2TM G2102 " ideal model delta sigma weight residual 132.18 146.63 -14.45 3.00e+00 1.11e-01 2.32e+01 angle pdb=" PB B2TM D2006 " pdb=" O3BB2TM D2006 " pdb=" PG B2TM D2006 " ideal model delta sigma weight residual 132.18 144.88 -12.70 3.00e+00 1.11e-01 1.79e+01 angle pdb=" N ARG F 172 " pdb=" CA ARG F 172 " pdb=" C ARG F 172 " ideal model delta sigma weight residual 111.28 106.93 4.35 1.09e+00 8.42e-01 1.59e+01 angle pdb=" N ASN D 737 " pdb=" CA ASN D 737 " pdb=" C ASN D 737 " ideal model delta sigma weight residual 111.74 106.46 5.28 1.35e+00 5.49e-01 1.53e+01 angle pdb=" C2' DA G 17 " pdb=" C1' DA G 17 " pdb=" N9 DA G 17 " ideal model delta sigma weight residual 113.50 119.32 -5.82 1.50e+00 4.44e-01 1.51e+01 ... (remaining 38518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.91: 16057 31.91 - 63.82: 1054 63.82 - 95.73: 93 95.73 - 127.64: 5 127.64 - 159.56: 8 Dihedral angle restraints: 17217 sinusoidal: 7765 harmonic: 9452 Sorted by residual: dihedral pdb=" CA SER A 46 " pdb=" C SER A 46 " pdb=" N SER A 47 " pdb=" CA SER A 47 " ideal model delta harmonic sigma weight residual 180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" O2BA2TM G2102 " pdb=" C1 A2TM G2102 " pdb=" PB A2TM G2102 " pdb=" PA A2TM G2102 " ideal model delta sinusoidal sigma weight residual 32.04 -168.40 -159.56 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" O1BA2TM G2102 " pdb=" C1 A2TM G2102 " pdb=" PB A2TM G2102 " pdb=" PA A2TM G2102 " ideal model delta sinusoidal sigma weight residual 160.42 -41.92 -157.66 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 17214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 3991 0.091 - 0.182: 340 0.182 - 0.273: 6 0.273 - 0.363: 1 0.363 - 0.454: 1 Chirality restraints: 4339 Sorted by residual: chirality pdb=" P DC H 42 " pdb=" OP1 DC H 42 " pdb=" OP2 DC H 42 " pdb=" O5' DC H 42 " both_signs ideal model delta sigma weight residual True 2.35 -2.80 -0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" C1' DA G 17 " pdb=" O4' DA G 17 " pdb=" C2' DA G 17 " pdb=" N9 DA G 17 " both_signs ideal model delta sigma weight residual False 2.42 2.13 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" P DA G 17 " pdb=" OP1 DA G 17 " pdb=" OP2 DA G 17 " pdb=" O5' DA G 17 " both_signs ideal model delta sigma weight residual True 2.35 -2.61 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 4336 not shown) Planarity restraints: 4774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1FAB4P G2101 " 0.058 2.00e-02 2.50e+03 2.66e-02 1.95e+01 pdb=" C2BAB4P G2101 " -0.008 2.00e-02 2.50e+03 pdb=" C4BAB4P G2101 " -0.014 2.00e-02 2.50e+03 pdb=" C5BAB4P G2101 " -0.013 2.00e-02 2.50e+03 pdb=" C6BAB4P G2101 " -0.006 2.00e-02 2.50e+03 pdb=" C8BAB4P G2101 " -0.020 2.00e-02 2.50e+03 pdb=" N1BAB4P G2101 " -0.006 2.00e-02 2.50e+03 pdb=" N3BAB4P G2101 " -0.010 2.00e-02 2.50e+03 pdb=" N6BAB4P G2101 " 0.053 2.00e-02 2.50e+03 pdb=" N7BAB4P G2101 " -0.019 2.00e-02 2.50e+03 pdb=" N9BAB4P G2101 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 247 " -0.053 5.00e-02 4.00e+02 8.08e-02 1.04e+01 pdb=" N PRO C 248 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 248 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 248 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT G 16 " 0.024 2.00e-02 2.50e+03 2.02e-02 1.02e+01 pdb=" N1 DT G 16 " -0.050 2.00e-02 2.50e+03 pdb=" C2 DT G 16 " 0.028 2.00e-02 2.50e+03 pdb=" O2 DT G 16 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DT G 16 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DT G 16 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT G 16 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DT G 16 " 0.005 2.00e-02 2.50e+03 pdb=" C7 DT G 16 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT G 16 " 0.001 2.00e-02 2.50e+03 ... (remaining 4771 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 128 2.55 - 3.13: 20119 3.13 - 3.72: 42827 3.72 - 4.31: 61576 4.31 - 4.90: 100683 Nonbonded interactions: 225333 Sorted by model distance: nonbonded pdb="MG B MG D2004 " pdb=" O1BB2TM D2006 " model vdw 1.958 2.170 nonbonded pdb="MG MG D2003 " pdb=" O3EAB4P G2101 " model vdw 2.031 2.170 nonbonded pdb=" OD1 ASP D 739 " pdb="MG MG D2003 " model vdw 2.042 2.170 nonbonded pdb=" O LYS D 840 " pdb="MG MG D2005 " model vdw 2.049 2.170 nonbonded pdb=" OD1 ASP D 743 " pdb="MG MG D2003 " model vdw 2.067 2.170 ... (remaining 225328 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 'A' selection = (chain 'B' and resid 4 through 231) } 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=0.50 max=1.00 mean=0.99 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: 13.360 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: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 37.770 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 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:7.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 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 : 0.004 0.079 28233 Z= 0.192 Angle : 0.712 14.452 38529 Z= 0.386 Chirality : 0.047 0.454 4339 Planarity : 0.009 0.119 4774 Dihedral : 19.447 159.556 11137 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.64 % Allowed : 24.91 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 0.57 (0.14), residues: 3271 helix: 1.20 (0.15), residues: 1239 sheet: -0.03 (0.24), residues: 457 loop : -0.05 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG D 988 TYR 0.037 0.001 TYR D 450 PHE 0.023 0.002 PHE B 65 TRP 0.017 0.002 TRP E 63 HIS 0.006 0.001 HIS D1364 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.19 (28226) covalent geometry : angle 0.71104 / 0.39 (38523) hydrogen bonds : bond 0.14361 / 9.70 ( 1287) hydrogen bonds : angle 5.91247 / 4.08 ( 3527) metal coordination : bond 0.00566 / 0.31 ( 7) metal coordination : angle 2.82027 / 1.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 303 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8042 (tp30) REVERT: B 76 VAL cc_start: 0.9171 (p) cc_final: 0.8943 (m) REVERT: E 80 VAL cc_start: 0.8867 (t) cc_final: 0.8659 (p) outliers start: 17 outliers final: 6 residues processed: 318 average time/residue: 0.9562 time to fit residues: 341.4007 Evaluate side-chains 178 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 171 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 890 VAL Chi-restraints excluded: chain D residue 1083 ASP Chi-restraints excluded: chain D residue 1422 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN B 227 ASN C 434 HIS D 737 ASN D 762 GLN D1235 GLN B D1364 HIS ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.070174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.055578 restraints weight = 237911.467| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 4.65 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28233 Z= 0.146 Angle : 0.605 7.896 38529 Z= 0.318 Chirality : 0.043 0.196 4339 Planarity : 0.005 0.066 4774 Dihedral : 15.752 143.368 4579 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.22 % Allowed : 25.13 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.15 (0.15), residues: 3271 helix: 1.71 (0.15), residues: 1262 sheet: 0.24 (0.24), residues: 453 loop : 0.24 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 675 TYR 0.018 0.001 TYR D1198 PHE 0.035 0.002 PHE D 403 TRP 0.010 0.001 TRP A 200 HIS 0.010 0.001 HIS D1364 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (28226) covalent geometry : angle 0.60429 / 0.32 (38523) hydrogen bonds : bond 0.04577 / 3.10 ( 1287) hydrogen bonds : angle 4.76529 / 3.28 ( 3527) metal coordination : bond 0.00331 / 0.19 ( 7) metal coordination : angle 2.31489 / 1.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 184 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1458 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8622 (mm-30) outliers start: 61 outliers final: 11 residues processed: 231 average time/residue: 0.7967 time to fit residues: 210.0367 Evaluate side-chains 174 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 932 GLU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1281 VAL Chi-restraints excluded: chain D residue 1292 VAL Chi-restraints excluded: chain D residue 1458 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 48 optimal weight: 0.8980 chunk 188 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 chunk 32 optimal weight: 0.0770 chunk 217 optimal weight: 0.9980 chunk 270 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 209 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN ** C1100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1037 GLN ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 269 ASN F 312 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.068863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.053847 restraints weight = 241729.457| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 4.32 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 28233 Z= 0.147 Angle : 0.566 7.658 38529 Z= 0.296 Chirality : 0.042 0.158 4339 Planarity : 0.005 0.058 4774 Dihedral : 15.334 144.506 4567 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.90 % Allowed : 24.84 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.33 (0.15), residues: 3271 helix: 1.82 (0.15), residues: 1265 sheet: 0.46 (0.24), residues: 436 loop : 0.34 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 675 TYR 0.021 0.001 TYR D1198 PHE 0.020 0.001 PHE D 403 TRP 0.010 0.001 TRP A 200 HIS 0.008 0.001 HIS F 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (28226) covalent geometry : angle 0.56590 / 0.30 (38523) hydrogen bonds : bond 0.04397 / 2.98 ( 1287) hydrogen bonds : angle 4.61131 / 3.18 ( 3527) metal coordination : bond 0.00321 / 0.18 ( 7) metal coordination : angle 1.98155 / 0.98 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 171 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1293 PHE cc_start: 0.6927 (OUTLIER) cc_final: 0.6666 (t80) REVERT: D 1362 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8794 (tttt) REVERT: E 31 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9218 (mp) outliers start: 52 outliers final: 11 residues processed: 213 average time/residue: 0.7999 time to fit residues: 195.4016 Evaluate side-chains 167 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 1083 ASP Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1293 PHE Chi-restraints excluded: chain D residue 1326 THR Chi-restraints excluded: chain D residue 1362 LYS Chi-restraints excluded: chain D residue 1408 ILE Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain F residue 93 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 53 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 264 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 308 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN B 128 HIS ** C1100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 GLN D1172 HIS F 269 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.067551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.045073 restraints weight = 214865.143| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 3.59 r_work: 0.2681 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 28233 Z= 0.172 Angle : 0.575 8.072 38529 Z= 0.300 Chirality : 0.043 0.154 4339 Planarity : 0.005 0.059 4774 Dihedral : 15.184 144.696 4566 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.00 % Allowed : 24.27 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.38 (0.15), residues: 3271 helix: 1.81 (0.15), residues: 1271 sheet: 0.53 (0.24), residues: 436 loop : 0.41 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 189 TYR 0.022 0.001 TYR D1198 PHE 0.013 0.002 PHE C 684 TRP 0.011 0.001 TRP D1434 HIS 0.008 0.001 HIS F 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (28226) covalent geometry : angle 0.57428 / 0.30 (38523) hydrogen bonds : bond 0.04503 / 3.04 ( 1287) hydrogen bonds : angle 4.58217 / 3.17 ( 3527) metal coordination : bond 0.00424 / 0.23 ( 7) metal coordination : angle 2.04620 / 1.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 LYS cc_start: 0.8847 (tppp) cc_final: 0.8521 (tmtt) REVERT: B 57 TYR cc_start: 0.8366 (t80) cc_final: 0.7863 (t80) REVERT: B 139 ASN cc_start: 0.8160 (p0) cc_final: 0.7839 (p0) REVERT: C 252 LYS cc_start: 0.8880 (ttpt) cc_final: 0.8659 (ttpt) REVERT: C 284 ARG cc_start: 0.8179 (mmm160) cc_final: 0.7951 (mmm160) REVERT: D 64 LYS cc_start: 0.8834 (ttmm) cc_final: 0.8349 (mptp) REVERT: D 823 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8983 (tm) REVERT: D 1087 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8682 (mpt90) REVERT: D 1362 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9063 (tttm) REVERT: E 89 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8211 (mtt) outliers start: 55 outliers final: 15 residues processed: 201 average time/residue: 0.8500 time to fit residues: 194.1127 Evaluate side-chains 165 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain C residue 564 MET Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 932 GLU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 463 GLN Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 1087 ARG Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain D residue 1326 THR Chi-restraints excluded: chain D residue 1362 LYS Chi-restraints excluded: chain E residue 89 MET Chi-restraints excluded: chain F residue 93 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 286 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 289 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 239 optimal weight: 4.9990 chunk 313 optimal weight: 5.9990 chunk 230 optimal weight: 0.9980 chunk 184 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN ** C1100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.066728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.044385 restraints weight = 198341.828| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.47 r_work: 0.2663 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 28233 Z= 0.196 Angle : 0.582 9.298 38529 Z= 0.304 Chirality : 0.044 0.239 4339 Planarity : 0.005 0.057 4774 Dihedral : 15.109 143.126 4566 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.04 % Allowed : 24.16 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.39 (0.15), residues: 3271 helix: 1.84 (0.15), residues: 1264 sheet: 0.56 (0.24), residues: 440 loop : 0.38 (0.16), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 189 TYR 0.022 0.001 TYR D1198 PHE 0.014 0.002 PHE C 896 TRP 0.012 0.001 TRP D1434 HIS 0.006 0.001 HIS F 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (28226) covalent geometry : angle 0.58163 / 0.30 (38523) hydrogen bonds : bond 0.04645 / 3.15 ( 1287) hydrogen bonds : angle 4.59746 / 3.18 ( 3527) metal coordination : bond 0.00482 / 0.27 ( 7) metal coordination : angle 2.00095 / 0.98 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 158 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 GLN cc_start: 0.8556 (mm110) cc_final: 0.8287 (mm110) REVERT: B 57 TYR cc_start: 0.8472 (t80) cc_final: 0.8157 (t80) REVERT: B 139 ASN cc_start: 0.8291 (p0) cc_final: 0.7919 (p0) REVERT: C 252 LYS cc_start: 0.8851 (ttpt) cc_final: 0.8601 (ttpt) REVERT: D 351 MET cc_start: 0.8753 (pmm) cc_final: 0.8512 (pmm) REVERT: D 823 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9038 (tm) REVERT: D 1362 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.9110 (tttm) REVERT: E 89 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8270 (mtt) outliers start: 56 outliers final: 18 residues processed: 203 average time/residue: 0.8472 time to fit residues: 196.1528 Evaluate side-chains 170 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain C residue 564 MET Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 932 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 1083 ASP Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain D residue 1326 THR Chi-restraints excluded: chain D residue 1362 LYS Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 89 MET Chi-restraints excluded: chain F residue 93 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 72 optimal weight: 3.9990 chunk 309 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 44 optimal weight: 0.0670 chunk 325 optimal weight: 2.9990 chunk 241 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 261 optimal weight: 0.7980 chunk 271 optimal weight: 1.9990 chunk 322 optimal weight: 3.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN ** C1100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.067409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.045096 restraints weight = 235003.554| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.81 r_work: 0.2673 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28233 Z= 0.136 Angle : 0.551 9.131 38529 Z= 0.287 Chirality : 0.042 0.179 4339 Planarity : 0.004 0.060 4774 Dihedral : 14.969 140.734 4566 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.47 % Allowed : 24.45 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.49 (0.15), residues: 3271 helix: 1.91 (0.15), residues: 1264 sheet: 0.57 (0.24), residues: 439 loop : 0.47 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 422 TYR 0.017 0.001 TYR D1198 PHE 0.016 0.001 PHE F 233 TRP 0.011 0.001 TRP A 200 HIS 0.006 0.001 HIS F 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (28226) covalent geometry : angle 0.54994 / 0.29 (38523) hydrogen bonds : bond 0.04077 / 2.75 ( 1287) hydrogen bonds : angle 4.46178 / 3.08 ( 3527) metal coordination : bond 0.00322 / 0.18 ( 7) metal coordination : angle 2.06000 / 1.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 GLN cc_start: 0.8573 (mm110) cc_final: 0.8280 (mm110) REVERT: B 5 LYS cc_start: 0.8919 (tppp) cc_final: 0.8584 (tmmt) REVERT: B 57 TYR cc_start: 0.8516 (t80) cc_final: 0.8240 (t80) REVERT: B 139 ASN cc_start: 0.8319 (p0) cc_final: 0.8016 (p0) REVERT: C 284 ARG cc_start: 0.8190 (mmm160) cc_final: 0.7904 (mmm160) REVERT: D 351 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8583 (pmm) REVERT: D 483 HIS cc_start: 0.7939 (t-90) cc_final: 0.7649 (t-90) REVERT: D 823 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9050 (tm) REVERT: E 69 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9055 (mm) REVERT: E 89 MET cc_start: 0.8645 (mtt) cc_final: 0.8310 (mtt) outliers start: 40 outliers final: 13 residues processed: 190 average time/residue: 0.8480 time to fit residues: 184.2915 Evaluate side-chains 167 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1129 THR Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain D residue 1326 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain F residue 207 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 150 optimal weight: 0.5980 chunk 198 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 237 optimal weight: 2.9990 chunk 84 optimal weight: 0.0770 chunk 206 optimal weight: 0.5980 chunk 290 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN C 506 ASN ** C1100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1323 GLN ** F 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.067471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.045067 restraints weight = 228503.816| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.73 r_work: 0.2681 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28233 Z= 0.131 Angle : 0.547 10.971 38529 Z= 0.284 Chirality : 0.042 0.146 4339 Planarity : 0.004 0.063 4774 Dihedral : 14.844 137.189 4566 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.40 % Allowed : 24.80 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.54 (0.15), residues: 3271 helix: 1.96 (0.15), residues: 1266 sheet: 0.59 (0.24), residues: 439 loop : 0.50 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 422 TYR 0.024 0.001 TYR C 275 PHE 0.017 0.001 PHE D1293 TRP 0.011 0.001 TRP A 200 HIS 0.006 0.001 HIS F 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (28226) covalent geometry : angle 0.54609 / 0.28 (38523) hydrogen bonds : bond 0.03949 / 2.67 ( 1287) hydrogen bonds : angle 4.40231 / 3.03 ( 3527) metal coordination : bond 0.00296 / 0.17 ( 7) metal coordination : angle 2.06012 / 1.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 LYS cc_start: 0.8887 (tppp) cc_final: 0.8594 (tmmt) REVERT: B 57 TYR cc_start: 0.8542 (t80) cc_final: 0.8276 (t80) REVERT: B 139 ASN cc_start: 0.8321 (p0) cc_final: 0.7990 (p0) REVERT: C 69 LEU cc_start: 0.9489 (tp) cc_final: 0.9246 (mt) REVERT: C 284 ARG cc_start: 0.8212 (mmm160) cc_final: 0.7847 (mmm160) REVERT: D 483 HIS cc_start: 0.7991 (t-90) cc_final: 0.7708 (t-90) REVERT: D 823 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9068 (tm) REVERT: E 69 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9054 (mm) REVERT: E 89 MET cc_start: 0.8677 (mtt) cc_final: 0.8408 (mtt) REVERT: E 90 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8713 (pp20) REVERT: F 349 LEU cc_start: 0.9083 (mt) cc_final: 0.8864 (mt) outliers start: 38 outliers final: 14 residues processed: 188 average time/residue: 0.8112 time to fit residues: 174.8999 Evaluate side-chains 167 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1129 THR Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain D residue 1326 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 93 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 227 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 286 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 266 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN ** C1100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.066644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.044183 restraints weight = 238416.057| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.81 r_work: 0.2652 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28233 Z= 0.172 Angle : 0.571 11.201 38529 Z= 0.297 Chirality : 0.043 0.145 4339 Planarity : 0.005 0.063 4774 Dihedral : 14.861 134.423 4566 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.32 % Allowed : 24.73 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.50 (0.15), residues: 3271 helix: 1.95 (0.15), residues: 1260 sheet: 0.65 (0.25), residues: 430 loop : 0.43 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 422 TYR 0.022 0.001 TYR C 275 PHE 0.018 0.001 PHE D 207 TRP 0.012 0.001 TRP D1434 HIS 0.005 0.001 HIS D1075 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (28226) covalent geometry : angle 0.57015 / 0.30 (38523) hydrogen bonds : bond 0.04327 / 2.92 ( 1287) hydrogen bonds : angle 4.45667 / 3.07 ( 3527) metal coordination : bond 0.00434 / 0.24 ( 7) metal coordination : angle 2.05547 / 0.98 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 LYS cc_start: 0.8871 (tppp) cc_final: 0.8598 (tmmt) REVERT: B 57 TYR cc_start: 0.8596 (t80) cc_final: 0.8378 (t80) REVERT: B 139 ASN cc_start: 0.8373 (p0) cc_final: 0.8014 (p0) REVERT: D 351 MET cc_start: 0.8747 (pmm) cc_final: 0.8514 (pmm) REVERT: D 483 HIS cc_start: 0.8029 (t-90) cc_final: 0.7730 (t-90) REVERT: D 823 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9080 (tm) REVERT: D 980 MET cc_start: 0.7953 (mmm) cc_final: 0.7708 (mmm) REVERT: E 87 LYS cc_start: 0.9110 (ptpp) cc_final: 0.8790 (ptpp) REVERT: E 89 MET cc_start: 0.8691 (mtt) cc_final: 0.8420 (mtt) REVERT: E 90 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8781 (pp20) REVERT: F 233 PHE cc_start: 0.7884 (m-80) cc_final: 0.7674 (m-80) REVERT: F 349 LEU cc_start: 0.9062 (mt) cc_final: 0.8852 (mt) outliers start: 36 outliers final: 15 residues processed: 184 average time/residue: 0.7722 time to fit residues: 163.4614 Evaluate side-chains 168 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 676 MET Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1129 THR Chi-restraints excluded: chain D residue 1326 THR Chi-restraints excluded: chain F residue 93 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 145 optimal weight: 0.6980 chunk 198 optimal weight: 3.9990 chunk 288 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 188 optimal weight: 0.8980 chunk 218 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 225 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 0.2980 chunk 206 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN C 506 ASN ** C1100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 HIS F 214 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.067461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.053261 restraints weight = 193200.288| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.76 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28233 Z= 0.120 Angle : 0.553 11.049 38529 Z= 0.286 Chirality : 0.042 0.169 4339 Planarity : 0.004 0.063 4774 Dihedral : 14.758 131.024 4566 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.11 % Allowed : 24.98 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.58 (0.15), residues: 3271 helix: 2.00 (0.15), residues: 1266 sheet: 0.64 (0.25), residues: 427 loop : 0.49 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 422 TYR 0.023 0.001 TYR C 275 PHE 0.019 0.001 PHE D 207 TRP 0.011 0.001 TRP A 200 HIS 0.006 0.001 HIS F 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (28226) covalent geometry : angle 0.55247 / 0.29 (38523) hydrogen bonds : bond 0.03794 / 2.56 ( 1287) hydrogen bonds : angle 4.34259 / 2.98 ( 3527) metal coordination : bond 0.00268 / 0.16 ( 7) metal coordination : angle 2.09710 / 1.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 MET cc_start: 0.9380 (ttm) cc_final: 0.9061 (ttm) REVERT: C 284 ARG cc_start: 0.7662 (mmm160) cc_final: 0.7453 (mmm160) REVERT: D 823 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9148 (tm) REVERT: F 349 LEU cc_start: 0.8839 (mt) cc_final: 0.8616 (mt) outliers start: 30 outliers final: 16 residues processed: 181 average time/residue: 0.8416 time to fit residues: 174.9426 Evaluate side-chains 167 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 676 MET Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 1083 ASP Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1129 THR Chi-restraints excluded: chain D residue 1326 THR Chi-restraints excluded: chain F residue 93 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 323 optimal weight: 2.9990 chunk 127 optimal weight: 0.0030 chunk 276 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 256 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 292 optimal weight: 0.9990 chunk 294 optimal weight: 0.9990 chunk 210 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 165 optimal weight: 0.5980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN ** C1100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.067455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.053586 restraints weight = 171764.995| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 4.03 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 28233 Z= 0.154 Angle : 0.689 61.598 38529 Z= 0.346 Chirality : 0.042 0.278 4339 Planarity : 0.004 0.065 4774 Dihedral : 14.765 131.013 4566 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.82 % Allowed : 25.27 % Favored : 73.91 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.57 (0.15), residues: 3271 helix: 1.99 (0.15), residues: 1266 sheet: 0.64 (0.25), residues: 427 loop : 0.49 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.000 ARG D 360 TYR 0.023 0.001 TYR C 275 PHE 0.029 0.001 PHE F 233 TRP 0.011 0.001 TRP A 200 HIS 0.006 0.001 HIS F 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (28226) covalent geometry : angle 0.68873 / 0.35 (38523) hydrogen bonds : bond 0.03809 / 2.57 ( 1287) hydrogen bonds : angle 4.34415 / 2.98 ( 3527) metal coordination : bond 0.00245 / 0.15 ( 7) metal coordination : angle 2.09555 / 1.07 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 MET cc_start: 0.9387 (ttm) cc_final: 0.9065 (ttm) REVERT: C 284 ARG cc_start: 0.7649 (mmm160) cc_final: 0.7442 (mmm160) REVERT: D 823 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9150 (tm) REVERT: F 349 LEU cc_start: 0.8839 (mt) cc_final: 0.8628 (mt) outliers start: 22 outliers final: 15 residues processed: 168 average time/residue: 0.7726 time to fit residues: 149.0405 Evaluate side-chains 166 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 676 MET Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1129 THR Chi-restraints excluded: chain D residue 1326 THR Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 213 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 288 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN C 506 ASN ** C1100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 GLN ** 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 = 0.3477 r_free = 0.3477 target = 0.067460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.045281 restraints weight = 232296.366| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.74 r_work: 0.2691 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 28233 Z= 0.154 Angle : 0.689 61.598 38529 Z= 0.346 Chirality : 0.042 0.278 4339 Planarity : 0.004 0.065 4774 Dihedral : 14.765 131.013 4566 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.64 % Allowed : 25.55 % Favored : 73.80 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.57 (0.15), residues: 3271 helix: 1.99 (0.15), residues: 1266 sheet: 0.64 (0.25), residues: 427 loop : 0.49 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.000 ARG D 360 TYR 0.023 0.001 TYR C 275 PHE 0.029 0.001 PHE F 233 TRP 0.011 0.001 TRP A 200 HIS 0.006 0.001 HIS F 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (28226) covalent geometry : angle 0.68873 / 0.35 (38523) hydrogen bonds : bond 0.03809 / 2.57 ( 1287) hydrogen bonds : angle 4.34415 / 2.98 ( 3527) metal coordination : bond 0.00245 / 0.15 ( 7) metal coordination : angle 2.09555 / 1.07 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10202.40 seconds wall clock time: 174 minutes 7.05 seconds (10447.05 seconds total)