Starting phenix.real_space_refine on Mon Sep 14 10:06:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pyj_13717/09_2026/7pyj_13717.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pyj_13717/09_2026/7pyj_13717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7pyj_13717/09_2026/7pyj_13717.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pyj_13717/09_2026/7pyj_13717.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pyj_13717/09_2026/7pyj_13717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pyj_13717/09_2026/7pyj_13717.map" model { file = "/net/cci-nas-00/data/ceres_data/7pyj_13717/09_2026/7pyj_13717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pyj_13717/09_2026/7pyj_13717.cif" } resolution = 4.2 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= 0.006 sd= 0.053 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 68 5.49 5 Mg 1 5.21 5 S 105 5.16 5 C 18090 2.51 5 N 5265 2.21 5 O 5831 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29362 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1775 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain: "B" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2076 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 6, 'ARG:plan': 5, 'GLU:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 111 Chain: "C" Number of atoms: 10577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10577 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 56, 'TRANS': 1283} Chain: "D" Number of atoms: 10375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10375 Classifications: {'peptide': 1334} Link IDs: {'PTRANS': 55, 'TRANS': 1278} Chain breaks: 2 Chain: "E" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "N" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 554 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "R" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 235 Classifications: {'RNAv2': 11} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 9} Chain: "T" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 611 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "F" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 2447 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 479} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1451 Unresolved non-hydrogen angles: 1853 Unresolved non-hydrogen dihedrals: 1145 Unresolved non-hydrogen chiralities: 145 Planarities with less than four sites: {'ASN:plan1': 19, 'GLU:plan': 56, 'ARG:plan': 33, 'PHE:plan': 14, 'TYR:plan': 6, 'GLN:plan1': 19, 'ASP:plan': 42, 'TRP:plan': 4, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 830 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20711 SG CYS D 814 98.693 53.166 106.585 1.00241.74 S ATOM 21276 SG CYS D 888 96.467 56.253 106.198 1.00217.46 S ATOM 21327 SG CYS D 895 97.687 54.495 103.089 1.00222.42 S ATOM 21348 SG CYS D 898 95.378 52.606 105.209 1.00222.56 S Time building chain proxies: 6.31, per 1000 atoms: 0.21 Number of scatterers: 29362 At special positions: 0 Unit cell: (191.84, 150.42, 183.12, 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 105 16.00 P 68 15.00 Mg 1 11.99 O 5831 8.00 N 5265 7.00 C 18090 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: 2.76 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " Number of angles added : 6 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7018 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 53 sheets defined 41.0% alpha, 14.0% beta 28 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 4.08 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.907A pdb=" N LEU A 39 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 removed outlier: 4.001A pdb=" N ILE A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 156 through 161 removed outlier: 3.633A pdb=" N SER A 161 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 230 removed outlier: 3.611A pdb=" N ALA A 216 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.505A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.974A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.550A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 4.022A pdb=" N LEU B 254 " --> pdb=" O ASP B 250 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG B 255 " --> pdb=" O PRO B 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 250 through 255' Processing helix chain 'B' and resid 263 through 271 removed outlier: 3.500A pdb=" N ASN B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 323 through 327 removed outlier: 3.933A pdb=" N ALA B 327 " --> pdb=" O ALA B 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 10 removed outlier: 4.153A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.958A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 57 removed outlier: 3.549A pdb=" N ALA C 51 " --> pdb=" O TYR C 47 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.677A pdb=" N CYS C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.706A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.084A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.924A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.540A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.834A pdb=" N ASP C 491 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 545 through 549 Processing helix chain 'C' and resid 551 through 555 Processing helix chain 'C' and resid 607 through 612 removed outlier: 3.596A pdb=" N GLU C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 607 through 612' Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 657 through 661 removed outlier: 3.819A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 688 removed outlier: 4.757A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 898 through 907 Processing helix chain 'C' and resid 942 through 980 removed outlier: 3.956A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 991 removed outlier: 4.280A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 986 through 991' Processing helix chain 'C' and resid 993 through 1000 Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.296A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1135 removed outlier: 3.732A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.619A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.525A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE C1164 " --> pdb=" O LEU C1161 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1160 through 1164' Processing helix chain 'C' and resid 1166 through 1176 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.652A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1293 Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 3.661A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C1309 " --> pdb=" O TYR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1334 removed outlier: 4.004A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY C1334 " --> pdb=" O ILE C1330 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 95 through 101 Processing helix chain 'D' and resid 113 through 119 removed outlier: 3.626A pdb=" N LEU D 117 " --> pdb=" O HIS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.933A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 173 through 176 Processing helix chain 'D' and resid 180 through 190 Processing helix chain 'D' and resid 193 through 207 removed outlier: 3.648A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.558A pdb=" N ILE D 238 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 263 through 286 removed outlier: 3.904A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 4.035A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 458 removed outlier: 3.771A pdb=" N CYS D 454 " --> pdb=" O HIS D 450 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 504 through 513 removed outlier: 3.986A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 540 removed outlier: 3.914A pdb=" N GLU D 534 " --> pdb=" O PRO D 530 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.663A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 636 removed outlier: 3.623A pdb=" N THR D 617 " --> pdb=" O GLY D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.007A pdb=" N GLU D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA D 657 " --> pdb=" O ILE D 653 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU D 658 " --> pdb=" O ILE D 654 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA D 659 " --> pdb=" O SER D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.149A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 729 removed outlier: 3.608A pdb=" N GLY D 729 " --> pdb=" O MET D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.214A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.607A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 removed outlier: 3.634A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 926 through 930 removed outlier: 3.789A pdb=" N LEU D 930 " --> pdb=" O GLY D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1138 through 1147 Processing helix chain 'D' and resid 1216 through 1225 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.594A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 4.444A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D1257 " --> pdb=" O ILE D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1291 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1324 Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1347 through 1354 Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 4.491A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.643A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 91 removed outlier: 3.619A pdb=" N GLU E 88 " --> pdb=" O THR E 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 10 removed outlier: 3.817A pdb=" N ALA F 7 " --> pdb=" O LYS F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 37 Processing helix chain 'F' and resid 70 through 74 removed outlier: 3.567A pdb=" N GLU F 74 " --> pdb=" O PRO F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 81 Processing helix chain 'F' and resid 82 through 84 No H-bonds generated for 'chain 'F' and resid 82 through 84' Processing helix chain 'F' and resid 103 through 132 Processing helix chain 'F' and resid 201 through 213 removed outlier: 3.766A pdb=" N LEU F 205 " --> pdb=" O LYS F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 253 Processing helix chain 'F' and resid 256 through 267 Processing helix chain 'F' and resid 279 through 288 Processing helix chain 'F' and resid 310 through 319 removed outlier: 3.941A pdb=" N GLN F 316 " --> pdb=" O GLY F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 333 Processing helix chain 'F' and resid 340 through 363 Processing helix chain 'F' and resid 366 through 377 removed outlier: 3.702A pdb=" N VAL F 372 " --> pdb=" O ASP F 368 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU F 376 " --> pdb=" O VAL F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 395 removed outlier: 4.113A pdb=" N GLU F 391 " --> pdb=" O PRO F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 426 Processing helix chain 'F' and resid 431 through 436 Processing helix chain 'F' and resid 441 through 450 Processing helix chain 'F' and resid 455 through 462 Processing helix chain 'F' and resid 463 through 468 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 484 through 492 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 104 removed outlier: 3.548A pdb=" N MET A 142 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.519A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 16 through 19 removed outlier: 3.803A pdb=" N MET B 205 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 109 removed outlier: 4.350A pdb=" N GLY B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU B 133 " --> pdb=" O GLY B 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.475A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 66 through 75 removed outlier: 5.295A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N ALA C 94 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N MET C 124 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU C 96 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL C 122 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL C 98 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLN C 120 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU C 100 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LYS C 118 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU C 102 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP C 116 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB3, first strand: chain 'C' and resid 154 through 159 Processing sheet with id=AB4, first strand: chain 'C' and resid 184 through 187 removed outlier: 4.228A pdb=" N ASP C 185 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG C 197 " --> pdb=" O ASP C 185 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 227 through 231 Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.412A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS C 260 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.112A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC2, first strand: chain 'C' and resid 633 through 637 removed outlier: 3.570A pdb=" N VAL C 634 " --> pdb=" O PHE C 645 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER C 643 " --> pdb=" O CYS C 636 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.779A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC6, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.862A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE C 804 " --> pdb=" O THR C1226 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 846 through 847 removed outlier: 6.059A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 882 through 884 Processing sheet with id=AC9, first strand: chain 'C' and resid 887 through 888 Processing sheet with id=AD1, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 6.271A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.736A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1335 through 1341 removed outlier: 4.016A pdb=" N GLU C1338 " --> pdb=" O LYS D 21 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE D 20 " --> pdb=" O ASP D1342 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.691A pdb=" N VAL D 90 " --> pdb=" O CYS D 85 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 104 through 111 removed outlier: 3.567A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AD7, first strand: chain 'D' and resid 253 through 254 removed outlier: 3.868A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 355 through 357 Processing sheet with id=AD9, first strand: chain 'D' and resid 526 through 527 removed outlier: 6.540A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU D 556 " --> pdb=" O VAL D 564 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 705 through 706 removed outlier: 4.252A pdb=" N THR D 705 " --> pdb=" O GLN D 716 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE3, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE4, first strand: chain 'D' and resid 842 through 843 removed outlier: 4.040A pdb=" N ARG D 842 " --> pdb=" O LEU D 864 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 957 through 961 Processing sheet with id=AE6, first strand: chain 'D' and resid 965 through 967 removed outlier: 3.728A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1025 through 1029 removed outlier: 7.182A pdb=" N THR D1029 " --> pdb=" O THR D1120 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR D1120 " --> pdb=" O THR D1029 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1033 through 1034 Processing sheet with id=AE9, first strand: chain 'D' and resid 1046 through 1050 Processing sheet with id=AF1, first strand: chain 'D' and resid 1077 through 1079 removed outlier: 3.955A pdb=" N TYR D1099 " --> pdb=" O LEU D1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1161 through 1162 Processing sheet with id=AF3, first strand: chain 'D' and resid 1173 through 1177 removed outlier: 4.269A pdb=" N TYR D1186 " --> pdb=" O ILE D1177 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1278 through 1279 removed outlier: 6.471A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 45 through 49 Processing sheet with id=AF6, first strand: chain 'F' and resid 137 through 146 removed outlier: 6.798A pdb=" N SER F 151 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL F 145 " --> pdb=" O ASN F 149 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASN F 149 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLU F 159 " --> pdb=" O ALA F 193 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU F 195 " --> pdb=" O GLU F 159 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL F 197 " --> pdb=" O VAL F 161 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU F 163 " --> pdb=" O VAL F 197 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY F 192 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 222 through 229 removed outlier: 6.805A pdb=" N ALA F 237 " --> pdb=" O LYS F 224 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA F 226 " --> pdb=" O LYS F 235 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LYS F 235 " --> pdb=" O ALA F 226 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ARG F 228 " --> pdb=" O ARG F 233 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ARG F 233 " --> pdb=" O ARG F 228 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA F 234 " --> pdb=" O ASP F 272 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL F 274 " --> pdb=" O ALA F 234 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE F 236 " --> pdb=" O VAL F 274 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 296 through 299 removed outlier: 3.537A pdb=" N ASP F 299 " --> pdb=" O THR F 304 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR F 304 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN F 337 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE F 307 " --> pdb=" O ASN F 337 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET F 339 " --> pdb=" O ILE F 307 " (cutoff:3.500A) 1183 hydrogen bonds defined for protein. 3330 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 7.66 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9818 1.34 - 1.46: 4907 1.46 - 1.58: 14851 1.58 - 1.70: 132 1.70 - 1.82: 182 Bond restraints: 29890 Sorted by residual: bond pdb=" C1' DC T 20 " pdb=" N1 DC T 20 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.20e+01 bond pdb=" C1' DC N 17 " pdb=" N1 DC N 17 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.07e+01 bond pdb=" C1' DT N 23 " pdb=" N1 DT N 23 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.06e+01 bond pdb=" C3' DC N 35 " pdb=" C2' DC N 35 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.96e+00 bond pdb=" C1' DC T 25 " pdb=" N1 DC T 25 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.75e+00 ... (remaining 29885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 40364 2.81 - 5.63: 362 5.63 - 8.44: 51 8.44 - 11.25: 4 11.25 - 14.07: 1 Bond angle restraints: 40782 Sorted by residual: angle pdb=" C GLY F 479 " pdb=" N ALA F 480 " pdb=" CA ALA F 480 " ideal model delta sigma weight residual 122.56 114.40 8.16 1.50e+00 4.44e-01 2.96e+01 angle pdb=" O4' DT T 2 " pdb=" C4' DT T 2 " pdb=" C3' DT T 2 " ideal model delta sigma weight residual 106.00 102.96 3.04 6.00e-01 2.78e+00 2.57e+01 angle pdb=" N3 DT T 13 " pdb=" C4 DT T 13 " pdb=" O4 DT T 13 " ideal model delta sigma weight residual 119.90 122.79 -2.89 6.00e-01 2.78e+00 2.32e+01 angle pdb=" C ALA F 11 " pdb=" N VAL F 12 " pdb=" CA VAL F 12 " ideal model delta sigma weight residual 121.70 130.35 -8.65 1.80e+00 3.09e-01 2.31e+01 angle pdb=" O4 DT T 13 " pdb=" C4 DT T 13 " pdb=" C5 DT T 13 " ideal model delta sigma weight residual 124.90 121.83 3.07 7.00e-01 2.04e+00 1.92e+01 ... (remaining 40777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 17653 35.75 - 71.50: 440 71.50 - 107.26: 23 107.26 - 143.01: 2 143.01 - 178.76: 2 Dihedral angle restraints: 18120 sinusoidal: 7240 harmonic: 10880 Sorted by residual: dihedral pdb=" C4' U R 4 " pdb=" C3' U R 4 " pdb=" C2' U R 4 " pdb=" C1' U R 4 " ideal model delta sinusoidal sigma weight residual 36.34 -38.54 74.89 1 3.10e+00 1.04e-01 7.39e+02 dihedral pdb=" O4' U R 4 " pdb=" C4' U R 4 " pdb=" C3' U R 4 " pdb=" C2' U R 4 " ideal model delta sinusoidal sigma weight residual -35.15 22.31 -57.46 1 4.00e+00 6.25e-02 2.77e+02 dihedral pdb=" CA PHE C 57 " pdb=" C PHE C 57 " pdb=" N PRO C 58 " pdb=" CA PRO C 58 " ideal model delta harmonic sigma weight residual -180.00 -104.70 -75.30 0 5.00e+00 4.00e-02 2.27e+02 ... (remaining 18117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 4463 0.094 - 0.188: 275 0.188 - 0.282: 17 0.282 - 0.376: 1 0.376 - 0.471: 1 Chirality restraints: 4757 Sorted by residual: chirality pdb=" P G R 14 " pdb=" OP1 G R 14 " pdb=" OP2 G R 14 " pdb=" O5' G R 14 " both_signs ideal model delta sigma weight residual True 2.17 -2.64 -0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" C3' U R 4 " pdb=" C4' U R 4 " pdb=" O3' U R 4 " pdb=" C2' U R 4 " both_signs ideal model delta sigma weight residual False -2.50 -2.83 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C2' U R 4 " pdb=" C3' U R 4 " pdb=" O2' U R 4 " pdb=" C1' U R 4 " both_signs ideal model delta sigma weight residual False -2.79 -2.53 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 4754 not shown) Planarity restraints: 5164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 29 " 0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO A 30 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 57 " 0.049 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO C 58 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO C 58 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 58 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 29 " 0.038 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO B 30 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " 0.032 5.00e-02 4.00e+02 ... (remaining 5161 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 617 2.65 - 3.21: 28430 3.21 - 3.77: 48134 3.77 - 4.34: 61635 4.34 - 4.90: 94907 Nonbonded interactions: 233723 Sorted by model distance: nonbonded pdb=" OD2 ASP D 460 " pdb="MG MG D1501 " model vdw 2.087 2.170 nonbonded pdb=" OD2 ASP D 462 " pdb="MG MG D1501 " model vdw 2.111 2.170 nonbonded pdb=" O3' G R 14 " pdb="MG MG D1501 " model vdw 2.113 2.170 nonbonded pdb=" O2 DC N 35 " pdb=" N2 DG T 5 " model vdw 2.163 2.496 nonbonded pdb=" OG1 THR D 816 " pdb=" OE2 GLU D 818 " model vdw 2.169 3.040 ... (remaining 233718 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 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: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 36.740 Find NCS groups from input model: 0.240 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 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 : 0.003 0.048 29894 Z= 0.211 Angle : 0.705 14.067 40788 Z= 0.398 Chirality : 0.048 0.471 4757 Planarity : 0.004 0.086 5164 Dihedral : 14.978 178.762 11102 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.66 % Favored : 93.28 % Rotamer: Outliers : 0.04 % Allowed : 0.33 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.06 % Twisted Proline : 1.34 % Twisted General : 0.03 % 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: -1.32 (0.13), residues: 3767 helix: 0.32 (0.14), residues: 1333 sheet: -1.81 (0.22), residues: 427 loop : -1.50 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 515 TYR 0.016 0.001 TYR C 70 PHE 0.038 0.002 PHE C 53 TRP 0.023 0.002 TRP C1276 HIS 0.005 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.21 (29890) covalent geometry : angle 0.70268 / 0.40 (40782) hydrogen bonds : bond 0.20093 / 13.77 ( 1253) hydrogen bonds : angle 7.48269 / 5.14 ( 3462) metal coordination : bond 0.01196 / 0.55 ( 4) metal coordination : angle 4.53847 / 2.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 TYR cc_start: 0.9288 (m-80) cc_final: 0.9034 (m-10) REVERT: B 212 ASP cc_start: 0.8814 (t0) cc_final: 0.8551 (t0) REVERT: C 427 ASP cc_start: 0.9394 (m-30) cc_final: 0.9178 (m-30) REVERT: C 519 ASN cc_start: 0.9367 (t0) cc_final: 0.8952 (t0) REVERT: C 653 MET cc_start: 0.9354 (tpt) cc_final: 0.8767 (tpt) REVERT: C 685 MET cc_start: 0.9650 (mpp) cc_final: 0.9034 (mpp) REVERT: C 800 MET cc_start: 0.8643 (pmm) cc_final: 0.8350 (pmm) REVERT: C 951 MET cc_start: 0.9646 (mmp) cc_final: 0.9356 (mmm) REVERT: C 1085 MET cc_start: 0.9307 (mmp) cc_final: 0.9033 (mmt) REVERT: C 1119 MET cc_start: 0.9499 (mmp) cc_final: 0.9212 (mmp) REVERT: C 1230 MET cc_start: 0.8591 (tmm) cc_final: 0.7478 (tmm) REVERT: C 1232 MET cc_start: 0.8769 (mmp) cc_final: 0.8348 (mmm) REVERT: C 1233 LEU cc_start: 0.9435 (mp) cc_final: 0.9151 (mp) REVERT: C 1273 MET cc_start: 0.9155 (mpp) cc_final: 0.8733 (mpp) REVERT: C 1287 LEU cc_start: 0.9776 (pp) cc_final: 0.9440 (pp) REVERT: D 102 MET cc_start: 0.8853 (ppp) cc_final: 0.8298 (ppp) REVERT: D 485 MET cc_start: 0.9549 (tpt) cc_final: 0.9112 (tpt) REVERT: D 622 ASP cc_start: 0.9372 (t0) cc_final: 0.9152 (t0) REVERT: D 644 MET cc_start: 0.9112 (mpp) cc_final: 0.8555 (mpp) REVERT: D 698 MET cc_start: 0.9660 (tpt) cc_final: 0.9373 (tpp) REVERT: D 725 MET cc_start: 0.9496 (mtp) cc_final: 0.9294 (mtp) REVERT: D 800 LEU cc_start: 0.9684 (mm) cc_final: 0.9474 (mm) REVERT: D 1254 GLU cc_start: 0.9201 (pt0) cc_final: 0.8325 (tp30) REVERT: D 1370 MET cc_start: 0.9505 (mmp) cc_final: 0.9168 (mmm) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.1615 time to fit residues: 58.4032 Evaluate side-chains 163 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.052793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.032138 restraints weight = 217672.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.032861 restraints weight = 127028.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.033546 restraints weight = 86781.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.034051 restraints weight = 65743.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.034407 restraints weight = 53394.679| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 29894 Z= 0.292 Angle : 0.720 16.836 40788 Z= 0.380 Chirality : 0.049 1.420 4757 Planarity : 0.005 0.087 5164 Dihedral : 14.425 178.869 4825 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.38 % Favored : 92.57 % Rotamer: Outliers : 0.07 % Allowed : 5.64 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.06 % Twisted Proline : 1.34 % Twisted General : 0.06 % 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: -1.30 (0.13), residues: 3767 helix: 0.39 (0.14), residues: 1393 sheet: -1.77 (0.24), residues: 383 loop : -1.62 (0.14), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 799 TYR 0.023 0.002 TYR D 631 PHE 0.025 0.002 PHE C 186 TRP 0.014 0.002 TRP C1276 HIS 0.007 0.002 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.29 (29890) covalent geometry : angle 0.71768 / 0.38 (40782) hydrogen bonds : bond 0.05769 / 4.01 ( 1253) hydrogen bonds : angle 5.95441 / 4.07 ( 3462) metal coordination : bond 0.01938 / 0.89 ( 4) metal coordination : angle 4.86681 / 2.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 173 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 68 TYR cc_start: 0.9342 (m-80) cc_final: 0.9037 (m-10) REVERT: B 212 ASP cc_start: 0.8833 (t0) cc_final: 0.8548 (t0) REVERT: C 653 MET cc_start: 0.9454 (tpt) cc_final: 0.8700 (tpt) REVERT: C 685 MET cc_start: 0.9670 (mpp) cc_final: 0.9414 (mmm) REVERT: C 800 MET cc_start: 0.8819 (pmm) cc_final: 0.8495 (pmm) REVERT: C 805 MET cc_start: 0.8648 (ppp) cc_final: 0.8367 (ppp) REVERT: C 951 MET cc_start: 0.9693 (mmp) cc_final: 0.9406 (mmm) REVERT: C 1119 MET cc_start: 0.9606 (mmp) cc_final: 0.9310 (mmp) REVERT: C 1131 MET cc_start: 0.9096 (mpp) cc_final: 0.8830 (mpp) REVERT: C 1170 MET cc_start: 0.9459 (ppp) cc_final: 0.9255 (ppp) REVERT: C 1230 MET cc_start: 0.8964 (tmm) cc_final: 0.7810 (tmm) REVERT: C 1232 MET cc_start: 0.8839 (mmp) cc_final: 0.8321 (mmm) REVERT: C 1233 LEU cc_start: 0.9336 (mp) cc_final: 0.8879 (mp) REVERT: C 1243 MET cc_start: 0.9398 (tmm) cc_final: 0.9187 (tmm) REVERT: C 1287 LEU cc_start: 0.9765 (pp) cc_final: 0.9421 (pp) REVERT: D 102 MET cc_start: 0.8884 (ppp) cc_final: 0.8306 (ppp) REVERT: D 622 ASP cc_start: 0.9424 (t0) cc_final: 0.9123 (t0) REVERT: D 644 MET cc_start: 0.9008 (mpp) cc_final: 0.8429 (mpp) REVERT: D 698 MET cc_start: 0.9664 (tpt) cc_final: 0.9389 (tpp) REVERT: D 725 MET cc_start: 0.9494 (mtp) cc_final: 0.9209 (tmm) REVERT: D 800 LEU cc_start: 0.9737 (mm) cc_final: 0.9378 (mm) REVERT: D 1254 GLU cc_start: 0.9155 (pt0) cc_final: 0.8473 (tp30) REVERT: D 1370 MET cc_start: 0.9513 (mmp) cc_final: 0.9238 (mmm) REVERT: E 15 ASN cc_start: 0.8723 (t0) cc_final: 0.7998 (t0) REVERT: E 18 ASP cc_start: 0.9488 (m-30) cc_final: 0.9095 (m-30) outliers start: 2 outliers final: 0 residues processed: 175 average time/residue: 0.1502 time to fit residues: 46.5334 Evaluate side-chains 144 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 54 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 374 optimal weight: 50.0000 chunk 245 optimal weight: 4.9990 chunk 319 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN A 227 GLN B 66 HIS ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.053063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.032421 restraints weight = 216542.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.033164 restraints weight = 124902.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.033916 restraints weight = 85256.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.034393 restraints weight = 63767.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.034749 restraints weight = 51805.752| |-----------------------------------------------------------------------------| r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29894 Z= 0.224 Angle : 0.641 12.630 40788 Z= 0.341 Chirality : 0.045 0.645 4757 Planarity : 0.004 0.084 5164 Dihedral : 14.447 178.482 4825 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.33 % Favored : 92.65 % Rotamer: Outliers : 0.04 % Allowed : 5.35 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.06 % Twisted Proline : 1.34 % Twisted General : 0.06 % 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: -1.21 (0.13), residues: 3767 helix: 0.56 (0.14), residues: 1396 sheet: -1.61 (0.24), residues: 406 loop : -1.67 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1048 TYR 0.019 0.002 TYR D 631 PHE 0.020 0.001 PHE C 186 TRP 0.013 0.002 TRP C1276 HIS 0.011 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.22 (29890) covalent geometry : angle 0.63793 / 0.34 (40782) hydrogen bonds : bond 0.05101 / 3.54 ( 1253) hydrogen bonds : angle 5.62662 / 3.85 ( 3462) metal coordination : bond 0.03060 / 1.55 ( 4) metal coordination : angle 5.10511 / 2.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 TYR cc_start: 0.9411 (m-80) cc_final: 0.9157 (m-10) REVERT: B 212 ASP cc_start: 0.8951 (t0) cc_final: 0.8667 (t0) REVERT: C 488 MET cc_start: 0.8612 (tmm) cc_final: 0.8213 (tmm) REVERT: C 653 MET cc_start: 0.9438 (tpt) cc_final: 0.8658 (tpt) REVERT: C 681 MET cc_start: 0.8871 (pmm) cc_final: 0.8628 (pmm) REVERT: C 725 GLN cc_start: 0.8606 (mt0) cc_final: 0.8367 (mt0) REVERT: C 800 MET cc_start: 0.8873 (pmm) cc_final: 0.8627 (pmm) REVERT: C 805 MET cc_start: 0.8642 (ppp) cc_final: 0.8255 (ppp) REVERT: C 834 GLN cc_start: 0.9622 (tt0) cc_final: 0.9230 (tp40) REVERT: C 951 MET cc_start: 0.9687 (mmp) cc_final: 0.9399 (mmm) REVERT: C 1119 MET cc_start: 0.9634 (mmp) cc_final: 0.9369 (mmp) REVERT: C 1131 MET cc_start: 0.9171 (mpp) cc_final: 0.8874 (mpp) REVERT: C 1170 MET cc_start: 0.9441 (ppp) cc_final: 0.9210 (ppp) REVERT: C 1230 MET cc_start: 0.9030 (tmm) cc_final: 0.8115 (tmm) REVERT: C 1232 MET cc_start: 0.8905 (mmp) cc_final: 0.8500 (mmm) REVERT: C 1243 MET cc_start: 0.9406 (tmm) cc_final: 0.9195 (tmm) REVERT: C 1273 MET cc_start: 0.9314 (mpp) cc_final: 0.8919 (mpp) REVERT: C 1287 LEU cc_start: 0.9781 (pp) cc_final: 0.9449 (pp) REVERT: D 485 MET cc_start: 0.9523 (tpt) cc_final: 0.9115 (tpt) REVERT: D 581 MET cc_start: 0.9032 (mmt) cc_final: 0.8804 (mmt) REVERT: D 622 ASP cc_start: 0.9409 (t0) cc_final: 0.9192 (t0) REVERT: D 644 MET cc_start: 0.9007 (mpp) cc_final: 0.8348 (mpp) REVERT: D 698 MET cc_start: 0.9659 (tpt) cc_final: 0.9375 (tpp) REVERT: D 800 LEU cc_start: 0.9740 (mm) cc_final: 0.9359 (mm) REVERT: D 1254 GLU cc_start: 0.9137 (pt0) cc_final: 0.8434 (tp30) REVERT: D 1370 MET cc_start: 0.9531 (mmp) cc_final: 0.9245 (mmm) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.1558 time to fit residues: 50.0936 Evaluate side-chains 142 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 207 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 380 optimal weight: 50.0000 chunk 292 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 333 optimal weight: 0.0870 chunk 230 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 251 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 HIS C 314 ASN ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 HIS ** 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 = 0.3313 r_free = 0.3313 target = 0.053665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.032816 restraints weight = 212484.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.033835 restraints weight = 121781.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.034565 restraints weight = 82775.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.035087 restraints weight = 62135.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.035460 restraints weight = 50255.545| |-----------------------------------------------------------------------------| r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29894 Z= 0.164 Angle : 0.601 12.091 40788 Z= 0.317 Chirality : 0.044 0.436 4757 Planarity : 0.004 0.095 5164 Dihedral : 14.418 178.074 4825 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.33 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.06 % Twisted Proline : 1.34 % Twisted General : 0.06 % 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: -1.12 (0.14), residues: 3767 helix: 0.68 (0.14), residues: 1414 sheet: -1.65 (0.23), residues: 414 loop : -1.64 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 91 TYR 0.018 0.001 TYR D 631 PHE 0.020 0.001 PHE C 186 TRP 0.011 0.001 TRP C 183 HIS 0.006 0.001 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (29890) covalent geometry : angle 0.59925 / 0.32 (40782) hydrogen bonds : bond 0.04667 / 3.23 ( 1253) hydrogen bonds : angle 5.38365 / 3.67 ( 3462) metal coordination : bond 0.02418 / 0.95 ( 4) metal coordination : angle 3.90084 / 2.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9369 (mt) cc_final: 0.9157 (mt) REVERT: B 68 TYR cc_start: 0.9367 (m-80) cc_final: 0.9120 (m-10) REVERT: B 212 ASP cc_start: 0.8940 (t0) cc_final: 0.8658 (t0) REVERT: C 130 MET cc_start: 0.8711 (mmp) cc_final: 0.8452 (mmp) REVERT: C 221 LEU cc_start: 0.9738 (tp) cc_final: 0.9509 (mm) REVERT: C 653 MET cc_start: 0.9423 (tpt) cc_final: 0.8742 (tpt) REVERT: C 685 MET cc_start: 0.9656 (mpp) cc_final: 0.9425 (mmm) REVERT: C 800 MET cc_start: 0.8843 (pmm) cc_final: 0.8621 (pmm) REVERT: C 805 MET cc_start: 0.8671 (ppp) cc_final: 0.8235 (ppp) REVERT: C 834 GLN cc_start: 0.9606 (tt0) cc_final: 0.9220 (tp40) REVERT: C 951 MET cc_start: 0.9695 (mmp) cc_final: 0.9401 (mmm) REVERT: C 1085 MET cc_start: 0.9117 (mmp) cc_final: 0.8713 (mmp) REVERT: C 1119 MET cc_start: 0.9666 (mmp) cc_final: 0.9411 (mmp) REVERT: C 1131 MET cc_start: 0.9181 (mpp) cc_final: 0.8901 (mpp) REVERT: C 1170 MET cc_start: 0.9465 (ppp) cc_final: 0.9221 (ppp) REVERT: C 1230 MET cc_start: 0.9057 (tmm) cc_final: 0.8121 (tmm) REVERT: C 1232 MET cc_start: 0.8877 (mmp) cc_final: 0.8487 (mmm) REVERT: C 1287 LEU cc_start: 0.9778 (pp) cc_final: 0.9434 (pp) REVERT: D 485 MET cc_start: 0.9530 (tpt) cc_final: 0.9160 (tpt) REVERT: D 581 MET cc_start: 0.9011 (mmt) cc_final: 0.8676 (mmt) REVERT: D 622 ASP cc_start: 0.9418 (t0) cc_final: 0.9197 (t0) REVERT: D 644 MET cc_start: 0.9114 (mpp) cc_final: 0.8425 (mpp) REVERT: D 698 MET cc_start: 0.9654 (tpt) cc_final: 0.9356 (tpp) REVERT: D 800 LEU cc_start: 0.9728 (mm) cc_final: 0.9294 (mm) REVERT: D 1254 GLU cc_start: 0.9097 (pt0) cc_final: 0.8372 (tp30) REVERT: D 1370 MET cc_start: 0.9528 (mmp) cc_final: 0.9234 (mmm) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1601 time to fit residues: 53.1036 Evaluate side-chains 152 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 136 optimal weight: 10.0000 chunk 286 optimal weight: 40.0000 chunk 330 optimal weight: 30.0000 chunk 346 optimal weight: 50.0000 chunk 314 optimal weight: 8.9990 chunk 363 optimal weight: 40.0000 chunk 74 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 355 optimal weight: 20.0000 chunk 197 optimal weight: 9.9990 overall best weight: 7.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 HIS C1236 ASN D 277 ASN ** D 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.051991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.031535 restraints weight = 219402.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.032131 restraints weight = 128183.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.032806 restraints weight = 88581.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.033284 restraints weight = 67167.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.033642 restraints weight = 54863.202| |-----------------------------------------------------------------------------| r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 29894 Z= 0.315 Angle : 0.733 14.015 40788 Z= 0.387 Chirality : 0.045 0.305 4757 Planarity : 0.005 0.097 5164 Dihedral : 14.567 177.518 4825 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.39 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.06 % Twisted Proline : 1.34 % Twisted General : 0.06 % 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: -1.48 (0.13), residues: 3767 helix: 0.29 (0.14), residues: 1427 sheet: -1.69 (0.24), residues: 409 loop : -1.82 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 799 TYR 0.019 0.002 TYR D 631 PHE 0.024 0.002 PHE C 186 TRP 0.010 0.002 TRP D1020 HIS 0.009 0.002 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.32 (29890) covalent geometry : angle 0.72873 / 0.39 (40782) hydrogen bonds : bond 0.05161 / 3.57 ( 1253) hydrogen bonds : angle 5.65623 / 3.86 ( 3462) metal coordination : bond 0.02290 / 1.05 ( 4) metal coordination : angle 6.49889 / 3.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 TYR cc_start: 0.9358 (m-80) cc_final: 0.9132 (m-10) REVERT: B 212 ASP cc_start: 0.8953 (t0) cc_final: 0.8729 (t0) REVERT: C 130 MET cc_start: 0.8733 (mmp) cc_final: 0.8468 (mmp) REVERT: C 221 LEU cc_start: 0.9755 (tp) cc_final: 0.9541 (mm) REVERT: C 443 ASP cc_start: 0.8448 (t70) cc_final: 0.8179 (t0) REVERT: C 459 MET cc_start: 0.9325 (mmp) cc_final: 0.9034 (mmm) REVERT: C 488 MET cc_start: 0.8568 (tmm) cc_final: 0.8092 (tmm) REVERT: C 653 MET cc_start: 0.9445 (tpt) cc_final: 0.8807 (tpp) REVERT: C 681 MET cc_start: 0.8933 (pmm) cc_final: 0.8712 (pmm) REVERT: C 800 MET cc_start: 0.8901 (pmm) cc_final: 0.8507 (pmm) REVERT: C 805 MET cc_start: 0.8790 (ppp) cc_final: 0.8349 (ppp) REVERT: C 834 GLN cc_start: 0.9617 (tt0) cc_final: 0.9268 (tp40) REVERT: C 951 MET cc_start: 0.9673 (mmp) cc_final: 0.9381 (mmm) REVERT: C 1119 MET cc_start: 0.9682 (mmp) cc_final: 0.9443 (mmp) REVERT: C 1131 MET cc_start: 0.9156 (mpp) cc_final: 0.8810 (mmm) REVERT: C 1170 MET cc_start: 0.9520 (ppp) cc_final: 0.9263 (ppp) REVERT: C 1230 MET cc_start: 0.9017 (tmm) cc_final: 0.8204 (tmm) REVERT: C 1232 MET cc_start: 0.8849 (mmp) cc_final: 0.8385 (mmm) REVERT: C 1287 LEU cc_start: 0.9792 (pp) cc_final: 0.9455 (pp) REVERT: D 644 MET cc_start: 0.9137 (mpp) cc_final: 0.8507 (mpp) REVERT: D 698 MET cc_start: 0.9650 (tpt) cc_final: 0.9342 (tpp) REVERT: D 725 MET cc_start: 0.9540 (mtp) cc_final: 0.9191 (tmm) REVERT: D 1254 GLU cc_start: 0.9122 (pt0) cc_final: 0.8358 (tp30) REVERT: D 1370 MET cc_start: 0.9547 (mmp) cc_final: 0.9283 (mmm) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1572 time to fit residues: 49.3023 Evaluate side-chains 143 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 365 optimal weight: 50.0000 chunk 95 optimal weight: 7.9990 chunk 343 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 chunk 337 optimal weight: 40.0000 chunk 288 optimal weight: 40.0000 chunk 179 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 338 optimal weight: 30.0000 chunk 221 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 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 = 0.3289 r_free = 0.3289 target = 0.052713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.031827 restraints weight = 215736.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.032799 restraints weight = 125006.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.033436 restraints weight = 84941.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.033904 restraints weight = 64011.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.034263 restraints weight = 52317.667| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29894 Z= 0.219 Angle : 0.639 14.717 40788 Z= 0.338 Chirality : 0.044 0.301 4757 Planarity : 0.004 0.095 5164 Dihedral : 14.540 176.977 4825 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.70 % Favored : 92.28 % Rotamer: Outliers : 0.04 % Allowed : 2.64 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.06 % Twisted Proline : 1.34 % Twisted General : 0.06 % 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: -1.30 (0.13), residues: 3767 helix: 0.52 (0.14), residues: 1416 sheet: -1.62 (0.24), residues: 413 loop : -1.77 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1284 TYR 0.019 0.002 TYR D 631 PHE 0.019 0.001 PHE C 186 TRP 0.010 0.001 TRP D1193 HIS 0.005 0.001 HIS C 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.22 (29890) covalent geometry : angle 0.63530 / 0.34 (40782) hydrogen bonds : bond 0.04650 / 3.22 ( 1253) hydrogen bonds : angle 5.42988 / 3.70 ( 3462) metal coordination : bond 0.01901 / 0.89 ( 4) metal coordination : angle 5.44361 / 2.74 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 TYR cc_start: 0.9338 (m-80) cc_final: 0.9082 (m-10) REVERT: B 212 ASP cc_start: 0.8921 (t0) cc_final: 0.8668 (t0) REVERT: C 130 MET cc_start: 0.8786 (mmp) cc_final: 0.8482 (mmp) REVERT: C 221 LEU cc_start: 0.9748 (tp) cc_final: 0.9535 (mm) REVERT: C 443 ASP cc_start: 0.8422 (t70) cc_final: 0.8135 (t0) REVERT: C 459 MET cc_start: 0.9355 (mmp) cc_final: 0.9137 (mmm) REVERT: C 488 MET cc_start: 0.8589 (tmm) cc_final: 0.8039 (tmm) REVERT: C 653 MET cc_start: 0.9456 (tpt) cc_final: 0.8879 (tpp) REVERT: C 681 MET cc_start: 0.9036 (pmm) cc_final: 0.8756 (pmm) REVERT: C 800 MET cc_start: 0.8933 (pmm) cc_final: 0.8498 (pmm) REVERT: C 805 MET cc_start: 0.8802 (ppp) cc_final: 0.8372 (ppp) REVERT: C 834 GLN cc_start: 0.9613 (tt0) cc_final: 0.9249 (tp40) REVERT: C 951 MET cc_start: 0.9688 (mmp) cc_final: 0.9401 (mmm) REVERT: C 1085 MET cc_start: 0.9177 (mmp) cc_final: 0.8780 (mmp) REVERT: C 1119 MET cc_start: 0.9695 (mmp) cc_final: 0.9463 (mmp) REVERT: C 1131 MET cc_start: 0.9173 (mpp) cc_final: 0.8855 (mpp) REVERT: C 1170 MET cc_start: 0.9519 (ppp) cc_final: 0.9229 (ppp) REVERT: C 1230 MET cc_start: 0.9035 (tmm) cc_final: 0.8252 (tmm) REVERT: C 1232 MET cc_start: 0.8904 (mmp) cc_final: 0.8421 (mmm) REVERT: C 1287 LEU cc_start: 0.9790 (pp) cc_final: 0.9453 (pp) REVERT: D 581 MET cc_start: 0.9117 (mmt) cc_final: 0.8665 (mmt) REVERT: D 622 ASP cc_start: 0.9400 (t0) cc_final: 0.9162 (t0) REVERT: D 644 MET cc_start: 0.9185 (mpp) cc_final: 0.8542 (mpp) REVERT: D 698 MET cc_start: 0.9647 (tpt) cc_final: 0.9324 (tpp) REVERT: D 725 MET cc_start: 0.9539 (mtp) cc_final: 0.9203 (tmm) REVERT: D 800 LEU cc_start: 0.9721 (mm) cc_final: 0.9330 (mm) REVERT: D 1254 GLU cc_start: 0.9091 (pt0) cc_final: 0.8351 (tp30) REVERT: D 1370 MET cc_start: 0.9546 (mmp) cc_final: 0.9275 (mmm) outliers start: 1 outliers final: 1 residues processed: 181 average time/residue: 0.1550 time to fit residues: 49.8235 Evaluate side-chains 150 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 349 optimal weight: 10.0000 chunk 37 optimal weight: 0.0170 chunk 186 optimal weight: 0.0670 chunk 190 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 311 optimal weight: 10.0000 chunk 378 optimal weight: 30.0000 chunk 149 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 overall best weight: 3.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 HIS ** 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 = 0.3304 r_free = 0.3304 target = 0.053324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.032380 restraints weight = 214452.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.033156 restraints weight = 123018.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.033885 restraints weight = 83694.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.034413 restraints weight = 62761.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.034813 restraints weight = 50886.903| |-----------------------------------------------------------------------------| r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29894 Z= 0.154 Angle : 0.610 13.646 40788 Z= 0.320 Chirality : 0.044 0.304 4757 Planarity : 0.004 0.093 5164 Dihedral : 14.493 176.631 4825 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.19 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.06 % Twisted Proline : 1.34 % Twisted General : 0.06 % 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: -1.13 (0.14), residues: 3767 helix: 0.67 (0.14), residues: 1425 sheet: -1.54 (0.24), residues: 411 loop : -1.69 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 137 TYR 0.017 0.001 TYR D 631 PHE 0.017 0.001 PHE C 186 TRP 0.008 0.001 TRP D1193 HIS 0.005 0.001 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (29890) covalent geometry : angle 0.60756 / 0.32 (40782) hydrogen bonds : bond 0.04443 / 3.09 ( 1253) hydrogen bonds : angle 5.29009 / 3.60 ( 3462) metal coordination : bond 0.01285 / 0.60 ( 4) metal coordination : angle 4.35513 / 2.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9372 (mt) cc_final: 0.9168 (mt) REVERT: A 82 LEU cc_start: 0.9757 (mm) cc_final: 0.9468 (tt) REVERT: B 51 MET cc_start: 0.9318 (mmp) cc_final: 0.9113 (mmm) REVERT: B 68 TYR cc_start: 0.9333 (m-80) cc_final: 0.9088 (m-10) REVERT: B 212 ASP cc_start: 0.8871 (t0) cc_final: 0.8626 (t0) REVERT: C 130 MET cc_start: 0.8803 (mmp) cc_final: 0.8406 (mmp) REVERT: C 221 LEU cc_start: 0.9740 (tp) cc_final: 0.9538 (mm) REVERT: C 443 ASP cc_start: 0.8405 (t70) cc_final: 0.8077 (t0) REVERT: C 488 MET cc_start: 0.8496 (tmm) cc_final: 0.7998 (tmm) REVERT: C 653 MET cc_start: 0.9422 (tpt) cc_final: 0.8884 (tpp) REVERT: C 681 MET cc_start: 0.9013 (pmm) cc_final: 0.8659 (pmm) REVERT: C 800 MET cc_start: 0.8840 (pmm) cc_final: 0.8364 (pmm) REVERT: C 805 MET cc_start: 0.8811 (ppp) cc_final: 0.8396 (ppp) REVERT: C 834 GLN cc_start: 0.9628 (tt0) cc_final: 0.9265 (tp40) REVERT: C 951 MET cc_start: 0.9703 (mmp) cc_final: 0.9426 (mmm) REVERT: C 1085 MET cc_start: 0.9165 (mmp) cc_final: 0.8700 (mmp) REVERT: C 1117 LEU cc_start: 0.9871 (mt) cc_final: 0.9659 (mt) REVERT: C 1119 MET cc_start: 0.9727 (mmp) cc_final: 0.9465 (mmp) REVERT: C 1131 MET cc_start: 0.9170 (mpp) cc_final: 0.8838 (mpp) REVERT: C 1170 MET cc_start: 0.9498 (ppp) cc_final: 0.9194 (ppp) REVERT: C 1230 MET cc_start: 0.8999 (tmm) cc_final: 0.8169 (tmm) REVERT: C 1232 MET cc_start: 0.8897 (mmp) cc_final: 0.8395 (mmm) REVERT: C 1287 LEU cc_start: 0.9776 (pp) cc_final: 0.9455 (pp) REVERT: C 1315 MET cc_start: 0.9260 (tmm) cc_final: 0.9021 (tmm) REVERT: D 485 MET cc_start: 0.9531 (tpt) cc_final: 0.9189 (tpt) REVERT: D 625 MET cc_start: 0.8971 (tmm) cc_final: 0.8669 (tmm) REVERT: D 644 MET cc_start: 0.9187 (mpp) cc_final: 0.8503 (mpp) REVERT: D 698 MET cc_start: 0.9652 (tpt) cc_final: 0.9323 (tpp) REVERT: D 725 MET cc_start: 0.9530 (mtp) cc_final: 0.9203 (tmm) REVERT: D 800 LEU cc_start: 0.9711 (mm) cc_final: 0.9281 (mm) REVERT: D 1254 GLU cc_start: 0.9090 (pt0) cc_final: 0.8332 (tp30) REVERT: D 1370 MET cc_start: 0.9546 (mmp) cc_final: 0.9278 (mmm) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1527 time to fit residues: 49.6247 Evaluate side-chains 154 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 227 optimal weight: 2.9990 chunk 310 optimal weight: 0.0870 chunk 176 optimal weight: 0.5980 chunk 170 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 258 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 368 optimal weight: 7.9990 chunk 191 optimal weight: 0.1980 chunk 371 optimal weight: 0.0030 overall best weight: 0.3368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 HIS C 450 ASN C 462 ASN C 551 HIS C 658 GLN ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.054817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.034151 restraints weight = 206550.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.035121 restraints weight = 116857.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.035930 restraints weight = 78824.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.036481 restraints weight = 57790.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.036872 restraints weight = 46416.041| |-----------------------------------------------------------------------------| r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 29894 Z= 0.113 Angle : 0.613 14.007 40788 Z= 0.315 Chirality : 0.045 0.301 4757 Planarity : 0.004 0.090 5164 Dihedral : 14.344 177.110 4825 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.21 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.06 % Twisted Proline : 1.34 % Twisted General : 0.06 % 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: -0.92 (0.14), residues: 3767 helix: 0.80 (0.14), residues: 1420 sheet: -1.39 (0.23), residues: 429 loop : -1.54 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 69 TYR 0.027 0.001 TYR D 457 PHE 0.015 0.001 PHE D 629 TRP 0.008 0.001 TRP C1276 HIS 0.008 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (29890) covalent geometry : angle 0.61122 / 0.32 (40782) hydrogen bonds : bond 0.04336 / 3.03 ( 1253) hydrogen bonds : angle 5.03954 / 3.44 ( 3462) metal coordination : bond 0.00520 / 0.25 ( 4) metal coordination : angle 3.61263 / 1.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9330 (mt) cc_final: 0.9122 (mt) REVERT: A 82 LEU cc_start: 0.9738 (mm) cc_final: 0.9472 (tt) REVERT: B 51 MET cc_start: 0.9247 (mmp) cc_final: 0.8971 (mmm) REVERT: B 68 TYR cc_start: 0.9332 (m-80) cc_final: 0.9070 (m-10) REVERT: B 205 MET cc_start: 0.8784 (ppp) cc_final: 0.8466 (tmm) REVERT: B 212 ASP cc_start: 0.8754 (t0) cc_final: 0.8517 (t0) REVERT: C 130 MET cc_start: 0.8758 (mmp) cc_final: 0.8215 (mmp) REVERT: C 221 LEU cc_start: 0.9713 (tp) cc_final: 0.9499 (mm) REVERT: C 443 ASP cc_start: 0.8331 (t70) cc_final: 0.7978 (t0) REVERT: C 488 MET cc_start: 0.8582 (tmm) cc_final: 0.8090 (tmm) REVERT: C 805 MET cc_start: 0.8794 (ppp) cc_final: 0.8112 (ppp) REVERT: C 834 GLN cc_start: 0.9640 (tt0) cc_final: 0.9078 (tm-30) REVERT: C 951 MET cc_start: 0.9730 (mmp) cc_final: 0.9456 (mmm) REVERT: C 1085 MET cc_start: 0.9034 (mmp) cc_final: 0.8498 (mmp) REVERT: C 1119 MET cc_start: 0.9691 (mmp) cc_final: 0.9459 (mmp) REVERT: C 1131 MET cc_start: 0.9198 (mpp) cc_final: 0.8865 (mpp) REVERT: C 1170 MET cc_start: 0.9491 (ppp) cc_final: 0.9188 (ppp) REVERT: C 1287 LEU cc_start: 0.9769 (pp) cc_final: 0.9471 (pp) REVERT: C 1315 MET cc_start: 0.9231 (tmm) cc_final: 0.8993 (tmm) REVERT: D 485 MET cc_start: 0.9515 (tpt) cc_final: 0.9164 (tpt) REVERT: D 505 ASP cc_start: 0.8220 (m-30) cc_final: 0.7920 (m-30) REVERT: D 581 MET cc_start: 0.9089 (mmt) cc_final: 0.8604 (mmt) REVERT: D 622 ASP cc_start: 0.9361 (t0) cc_final: 0.8963 (t0) REVERT: D 644 MET cc_start: 0.9197 (mpp) cc_final: 0.8464 (mpp) REVERT: D 698 MET cc_start: 0.9661 (tpt) cc_final: 0.9339 (tpp) REVERT: D 725 MET cc_start: 0.9556 (mtp) cc_final: 0.9327 (mtp) REVERT: D 1254 GLU cc_start: 0.9094 (pt0) cc_final: 0.8308 (tp30) REVERT: D 1370 MET cc_start: 0.9533 (mmp) cc_final: 0.9251 (mmm) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.1560 time to fit residues: 54.7727 Evaluate side-chains 163 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 44 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 244 optimal weight: 0.1980 chunk 227 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 79 optimal weight: 0.0050 chunk 293 optimal weight: 40.0000 chunk 40 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 overall best weight: 4.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN E 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.053321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.032830 restraints weight = 210448.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.033643 restraints weight = 122481.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.034378 restraints weight = 83991.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.034927 restraints weight = 63269.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.035313 restraints weight = 50862.590| |-----------------------------------------------------------------------------| r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29894 Z= 0.184 Angle : 0.614 13.180 40788 Z= 0.322 Chirality : 0.044 0.308 4757 Planarity : 0.004 0.090 5164 Dihedral : 14.367 177.794 4825 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.01 % Favored : 92.97 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.06 % Twisted Proline : 1.34 % Twisted General : 0.03 % 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: -0.94 (0.14), residues: 3767 helix: 0.79 (0.14), residues: 1441 sheet: -1.45 (0.24), residues: 419 loop : -1.56 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 799 TYR 0.014 0.001 TYR D 631 PHE 0.019 0.001 PHE C 405 TRP 0.021 0.002 TRP D1193 HIS 0.005 0.001 HIS D 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 (29890) covalent geometry : angle 0.61260 / 0.32 (40782) hydrogen bonds : bond 0.04393 / 3.07 ( 1253) hydrogen bonds : angle 5.12649 / 3.51 ( 3462) metal coordination : bond 0.01416 / 0.66 ( 4) metal coordination : angle 3.82873 / 1.98 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9368 (mt) cc_final: 0.9167 (mt) REVERT: B 51 MET cc_start: 0.9322 (mmp) cc_final: 0.9082 (mmm) REVERT: B 68 TYR cc_start: 0.9316 (m-80) cc_final: 0.9077 (m-10) REVERT: B 205 MET cc_start: 0.8809 (ppp) cc_final: 0.8321 (tmm) REVERT: B 212 ASP cc_start: 0.8823 (t0) cc_final: 0.8598 (t0) REVERT: C 130 MET cc_start: 0.8837 (mmp) cc_final: 0.8360 (mmp) REVERT: C 443 ASP cc_start: 0.8358 (t70) cc_final: 0.8010 (t0) REVERT: C 459 MET cc_start: 0.9286 (mmp) cc_final: 0.9068 (mmm) REVERT: C 488 MET cc_start: 0.8532 (tmm) cc_final: 0.7953 (tmm) REVERT: C 653 MET cc_start: 0.9261 (tpt) cc_final: 0.8266 (tpt) REVERT: C 681 MET cc_start: 0.9089 (pmm) cc_final: 0.8740 (pmm) REVERT: C 805 MET cc_start: 0.8783 (ppp) cc_final: 0.8310 (ppp) REVERT: C 834 GLN cc_start: 0.9626 (tt0) cc_final: 0.9271 (tp40) REVERT: C 951 MET cc_start: 0.9690 (mmp) cc_final: 0.9404 (mmm) REVERT: C 1085 MET cc_start: 0.9178 (mmp) cc_final: 0.8906 (mmp) REVERT: C 1119 MET cc_start: 0.9692 (mmp) cc_final: 0.9468 (mmp) REVERT: C 1131 MET cc_start: 0.9216 (mpp) cc_final: 0.8926 (mpp) REVERT: C 1170 MET cc_start: 0.9491 (ppp) cc_final: 0.9186 (ppp) REVERT: C 1230 MET cc_start: 0.8965 (tmm) cc_final: 0.7780 (tmm) REVERT: C 1232 MET cc_start: 0.8762 (mmp) cc_final: 0.8488 (mmm) REVERT: C 1287 LEU cc_start: 0.9771 (pp) cc_final: 0.9462 (pp) REVERT: C 1315 MET cc_start: 0.9258 (tmm) cc_final: 0.9048 (tmm) REVERT: D 505 ASP cc_start: 0.8187 (m-30) cc_final: 0.7914 (m-30) REVERT: D 622 ASP cc_start: 0.9435 (t0) cc_final: 0.9140 (t0) REVERT: D 644 MET cc_start: 0.9174 (mpp) cc_final: 0.8437 (mpp) REVERT: D 698 MET cc_start: 0.9650 (tpt) cc_final: 0.9315 (tpp) REVERT: D 725 MET cc_start: 0.9533 (mtp) cc_final: 0.9322 (mtp) REVERT: D 1370 MET cc_start: 0.9544 (mmp) cc_final: 0.9269 (mmm) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1564 time to fit residues: 50.9403 Evaluate side-chains 155 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 341 optimal weight: 50.0000 chunk 226 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 267 optimal weight: 4.9990 chunk 273 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 86 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 50 optimal weight: 0.0020 overall best weight: 4.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 658 GLN E 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.053271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.032575 restraints weight = 212317.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.033317 restraints weight = 123011.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.034058 restraints weight = 85071.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.034559 restraints weight = 64148.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.034934 restraints weight = 52019.366| |-----------------------------------------------------------------------------| r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 29894 Z= 0.179 Angle : 0.619 13.672 40788 Z= 0.324 Chirality : 0.044 0.308 4757 Planarity : 0.004 0.090 5164 Dihedral : 14.385 177.758 4825 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.09 % Favored : 92.89 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.06 % Twisted Proline : 1.34 % Twisted General : 0.06 % 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: -0.96 (0.14), residues: 3767 helix: 0.78 (0.14), residues: 1438 sheet: -1.45 (0.24), residues: 417 loop : -1.58 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 799 TYR 0.020 0.001 TYR D1282 PHE 0.020 0.001 PHE C 405 TRP 0.025 0.002 TRP D1193 HIS 0.005 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.18 (29890) covalent geometry : angle 0.61700 / 0.32 (40782) hydrogen bonds : bond 0.04331 / 3.03 ( 1253) hydrogen bonds : angle 5.13956 / 3.51 ( 3462) metal coordination : bond 0.01440 / 0.67 ( 4) metal coordination : angle 3.77172 / 1.99 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.9739 (mm) cc_final: 0.9444 (tt) REVERT: B 51 MET cc_start: 0.9321 (mmp) cc_final: 0.9093 (mmm) REVERT: B 68 TYR cc_start: 0.9330 (m-80) cc_final: 0.9088 (m-10) REVERT: B 212 ASP cc_start: 0.8836 (t0) cc_final: 0.8623 (t0) REVERT: C 130 MET cc_start: 0.8826 (mmp) cc_final: 0.8338 (mmp) REVERT: C 443 ASP cc_start: 0.8286 (t70) cc_final: 0.7941 (t0) REVERT: C 488 MET cc_start: 0.8522 (tmm) cc_final: 0.7961 (tmm) REVERT: C 681 MET cc_start: 0.9061 (pmm) cc_final: 0.8677 (pmm) REVERT: C 805 MET cc_start: 0.8812 (ppp) cc_final: 0.8335 (ppp) REVERT: C 834 GLN cc_start: 0.9631 (tt0) cc_final: 0.9271 (tp40) REVERT: C 951 MET cc_start: 0.9706 (mmp) cc_final: 0.9423 (mmm) REVERT: C 1085 MET cc_start: 0.9215 (mmp) cc_final: 0.8943 (mmp) REVERT: C 1119 MET cc_start: 0.9690 (mmp) cc_final: 0.9448 (mmp) REVERT: C 1131 MET cc_start: 0.9222 (mpp) cc_final: 0.8933 (mpp) REVERT: C 1170 MET cc_start: 0.9519 (ppp) cc_final: 0.9226 (ppp) REVERT: C 1230 MET cc_start: 0.8953 (tmm) cc_final: 0.7646 (tmm) REVERT: C 1232 MET cc_start: 0.8737 (mmp) cc_final: 0.8489 (mmm) REVERT: C 1287 LEU cc_start: 0.9778 (pp) cc_final: 0.9466 (pp) REVERT: D 485 MET cc_start: 0.9467 (tpt) cc_final: 0.9175 (tpt) REVERT: D 622 ASP cc_start: 0.9412 (t0) cc_final: 0.9138 (t0) REVERT: D 644 MET cc_start: 0.9210 (mpp) cc_final: 0.8437 (mpp) REVERT: D 698 MET cc_start: 0.9660 (tpt) cc_final: 0.9341 (tpp) REVERT: D 725 MET cc_start: 0.9534 (mtp) cc_final: 0.9318 (mtp) REVERT: D 772 TYR cc_start: 0.9266 (t80) cc_final: 0.9043 (t80) REVERT: D 1370 MET cc_start: 0.9537 (mmp) cc_final: 0.9269 (mmm) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1558 time to fit residues: 49.1199 Evaluate side-chains 149 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 44 optimal weight: 8.9990 chunk 206 optimal weight: 9.9990 chunk 232 optimal weight: 10.0000 chunk 359 optimal weight: 20.0000 chunk 230 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 288 optimal weight: 30.0000 chunk 362 optimal weight: 20.0000 chunk 120 optimal weight: 0.7980 chunk 82 optimal weight: 30.0000 chunk 350 optimal weight: 0.5980 overall best weight: 4.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 ASN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.053006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.032121 restraints weight = 214353.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.032858 restraints weight = 123791.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.033600 restraints weight = 83979.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.034066 restraints weight = 63339.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.034404 restraints weight = 51859.233| |-----------------------------------------------------------------------------| r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29894 Z= 0.192 Angle : 0.629 13.489 40788 Z= 0.330 Chirality : 0.044 0.310 4757 Planarity : 0.004 0.090 5164 Dihedral : 14.423 177.678 4825 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.65 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.06 % Twisted Proline : 1.34 % Twisted General : 0.03 % 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: -1.02 (0.14), residues: 3767 helix: 0.71 (0.14), residues: 1440 sheet: -1.47 (0.23), residues: 427 loop : -1.61 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 220 TYR 0.015 0.001 TYR D 631 PHE 0.020 0.001 PHE C 405 TRP 0.035 0.002 TRP D1193 HIS 0.004 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 (29890) covalent geometry : angle 0.62731 / 0.33 (40782) hydrogen bonds : bond 0.04391 / 3.07 ( 1253) hydrogen bonds : angle 5.17812 / 3.53 ( 3462) metal coordination : bond 0.01537 / 0.72 ( 4) metal coordination : angle 3.87410 / 2.03 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4939.39 seconds wall clock time: 86 minutes 21.38 seconds (5181.38 seconds total)