Starting phenix.real_space_refine on Mon Sep 14 03:51:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6jbq_9792/09_2026/6jbq_9792.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jbq_9792/09_2026/6jbq_9792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6jbq_9792/09_2026/6jbq_9792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jbq_9792/09_2026/6jbq_9792.map" model { file = "/net/cci-nas-00/data/ceres_data/6jbq_9792/09_2026/6jbq_9792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jbq_9792/09_2026/6jbq_9792.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6jbq_9792/09_2026/6jbq_9792.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6jbq_9792/09_2026/6jbq_9792.cif" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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 100 5.49 5 Mg 1 5.21 5 S 110 5.16 5 C 17361 2.51 5 N 4982 2.21 5 O 5607 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.16s 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: 28163 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1659 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1687 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 10320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1312, 10320 Classifications: {'peptide': 1312} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1256} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 10331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10331 Classifications: {'peptide': 1335} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1279} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1483 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 8, 'TRANS': 177} Chain: "G" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 976 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DG:plan': 1, ' DG:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 975 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 102 Classifications: {'RNAv2': 5} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna3p': 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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 14115 SG CYS D 70 108.666 53.521 59.698 1.00 82.04 S ATOM 14129 SG CYS D 72 110.161 52.724 56.967 1.00 89.71 S ATOM 14237 SG CYS D 85 112.115 53.653 60.075 1.00 91.35 S ATOM 14257 SG CYS D 88 111.598 56.634 58.806 1.00 81.03 S ATOM 19909 SG CYS D 814 84.362 73.965 120.932 1.00 62.71 S ATOM 20468 SG CYS D 888 83.493 75.628 116.538 1.00 50.62 S ATOM 20519 SG CYS D 895 84.827 72.639 118.258 1.00 46.75 S ATOM 20540 SG CYS D 898 81.075 75.142 119.104 1.00 44.42 S Time building chain proxies: 5.38, per 1000 atoms: 0.19 Number of scatterers: 28163 At special positions: 0 Unit cell: (133.848, 163.254, 159.198, 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 110 16.00 P 100 15.00 Mg 1 11.99 O 5607 8.00 N 4982 7.00 C 17361 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: 2.31 Conformation dependent library (CDL) restraints added in 962.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " Number of angles added : 12 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6192 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 51 sheets defined 36.9% alpha, 14.8% beta 26 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.542A pdb=" N LEU A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 removed outlier: 3.707A pdb=" N ALA A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.635A pdb=" N PHE A 231 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A 232 " --> pdb=" O GLU A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 232' Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.644A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN B 41 " --> pdb=" O HIS B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.585A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 4 through 9 removed outlier: 3.676A pdb=" N LYS C 9 " --> pdb=" O TYR C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 39 removed outlier: 3.668A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 4.158A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE C 57 " --> pdb=" O PHE C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 163 through 167 removed outlier: 3.674A pdb=" N SER C 166 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER C 167 " --> pdb=" O THR C 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 163 through 167' Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.555A pdb=" N PHE C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 291 through 294 removed outlier: 3.523A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 291 through 294' Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.914A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 359 through 371 Processing helix chain 'C' and resid 379 through 389 removed outlier: 4.041A 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 438 removed outlier: 3.640A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) 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 480 removed outlier: 3.550A pdb=" N ASN C 462 " --> pdb=" O GLU C 458 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN C 463 " --> pdb=" O MET C 459 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 508 removed outlier: 3.518A pdb=" N ALA C 501 " --> pdb=" O PRO C 497 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 527 removed outlier: 4.019A pdb=" N LYS C 527 " --> pdb=" O GLU C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 4.086A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 684 Processing helix chain 'C' and resid 685 through 689 removed outlier: 3.712A pdb=" N GLN C 688 " --> pdb=" O MET C 685 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA C 689 " --> pdb=" O GLN C 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 685 through 689' Processing helix chain 'C' and resid 704 through 712 removed outlier: 3.825A pdb=" N ALA C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER C 712 " --> pdb=" O VAL C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 825 removed outlier: 4.248A pdb=" N VAL C 823 " --> pdb=" O SER C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 864 removed outlier: 3.633A pdb=" N SER C 863 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 860 through 864' Processing helix chain 'C' and resid 896 through 907 removed outlier: 4.005A pdb=" N LEU C 902 " --> pdb=" O GLU C 898 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 907 " --> pdb=" O ARG C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 979 removed outlier: 3.991A pdb=" N LEU C 979 " --> pdb=" O ILE C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 1010 through 1038 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.617A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.853A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.661A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1167 through 1176 removed outlier: 4.224A pdb=" N ARG C1171 " --> pdb=" O GLU C1167 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.661A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.513A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP C1276 " --> pdb=" O GLU C1272 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1300 through 1310 removed outlier: 3.573A pdb=" N VAL C1309 " --> pdb=" O TYR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1321 through 1332 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.739A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG D 98 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG D 99 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU D 100 " --> pdb=" O VAL D 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 94 through 100' Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.609A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 168 Processing helix chain 'D' and resid 181 through 191 Processing helix chain 'D' and resid 194 through 208 Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.799A pdb=" N ALA D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE D 227 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 264 through 283 removed outlier: 4.248A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.615A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 341 removed outlier: 3.608A pdb=" N ASN D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.590A pdb=" N PHE D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 removed outlier: 3.608A pdb=" N ALA D 397 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU D 404 " --> pdb=" O MET D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 416 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 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 503 through 515 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.527A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.779A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 592 " --> pdb=" O TYR D 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 588 through 592' Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.826A pdb=" N VAL D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 702 removed outlier: 4.215A pdb=" N ILE D 683 " --> pdb=" O TYR D 679 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP D 684 " --> pdb=" O ASN D 680 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE D 685 " --> pdb=" O LYS D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 removed outlier: 3.551A pdb=" N SER D 728 " --> pdb=" O MET D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.539A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.782A pdb=" N LYS D 781 " --> pdb=" O HIS D 777 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY D 782 " --> pdb=" O GLY D 778 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR D 786 " --> pdb=" O GLY D 782 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 Processing helix chain 'D' and resid 865 through 876 removed outlier: 3.531A pdb=" N CYS D 869 " --> pdb=" O HIS D 865 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP D 870 " --> pdb=" O GLU D 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 925 removed outlier: 4.082A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 923 " --> pdb=" O ALA D 919 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 removed outlier: 3.577A pdb=" N PHE D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 3.649A pdb=" N ARG D1222 " --> pdb=" O HIS D1218 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1245 removed outlier: 3.665A pdb=" N THR D1230 " --> pdb=" O VAL D1226 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.347A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1292 removed outlier: 4.200A pdb=" N GLU D1291 " --> pdb=" O ILE D1287 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU D1292 " --> pdb=" O ALA D1288 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1313 removed outlier: 3.926A pdb=" N SER D1313 " --> pdb=" O ILE D1309 " (cutoff:3.500A) Processing helix chain 'D' and resid 1319 through 1324 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.675A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY D1339 " --> pdb=" O ALA D1335 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1354 removed outlier: 3.554A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1361 through 1371 removed outlier: 3.893A 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 17 through 32 removed outlier: 3.846A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 62 through 80 removed outlier: 3.560A pdb=" N VAL E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 17 Processing helix chain 'F' and resid 21 through 38 removed outlier: 3.947A pdb=" N LEU F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG F 28 " --> pdb=" O LEU F 24 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N HIS F 31 " --> pdb=" O VAL F 27 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LYS F 32 " --> pdb=" O ARG F 28 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER F 38 " --> pdb=" O ALA F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 59 removed outlier: 4.189A pdb=" N VAL F 49 " --> pdb=" O ASP F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 64 removed outlier: 3.633A pdb=" N SER F 63 " --> pdb=" O ALA F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 3.927A pdb=" N TRP F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 136 Processing helix chain 'F' and resid 139 through 150 Processing helix chain 'F' and resid 155 through 163 removed outlier: 3.629A pdb=" N ILE F 159 " --> pdb=" O SER F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 186 removed outlier: 3.696A pdb=" N VAL F 170 " --> pdb=" O PRO F 166 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS F 184 " --> pdb=" O ALA F 180 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN F 186 " --> pdb=" O ASP F 182 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 removed outlier: 4.089A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU A 198 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ALA A 189 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS A 200 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL A 187 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL A 202 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR A 185 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLU A 204 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE A 183 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU A 206 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 61 removed outlier: 6.403A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (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 104 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 109 Processing sheet with id=AA6, first strand: chain 'A' and resid 152 through 153 removed outlier: 4.291A pdb=" N VAL A 153 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 175 " --> pdb=" O VAL A 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 20 removed outlier: 5.460A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL B 19 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N HIS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 104 removed outlier: 3.955A pdb=" N LYS B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 140 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N GLY B 151 " --> pdb=" O PRO B 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 97 through 104 removed outlier: 3.955A pdb=" N LYS B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 140 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 151 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA B 175 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AB2, first strand: chain 'B' and resid 107 through 111 removed outlier: 3.569A pdb=" N GLY B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.657A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 71 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET C 124 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.826A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.861A pdb=" N SER C 147 " --> pdb=" O ARG C 529 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 160 removed outlier: 3.505A pdb=" N ASN C 173 " --> pdb=" O ASP C 158 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE C 188 " --> pdb=" O TYR C 172 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 228 through 230 Processing sheet with id=AB8, first strand: chain 'C' and resid 239 through 240 removed outlier: 3.664A pdb=" N MET C 239 " --> pdb=" O ILE C 285 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.818A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 296 through 297 removed outlier: 4.569A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 301 through 302 removed outlier: 7.756A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE C 310 " --> pdb=" O TYR C 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.518A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS C 593 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.518A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 623 through 624 removed outlier: 3.676A pdb=" N HIS C 628 " --> pdb=" O ASP C 624 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 634 through 637 Processing sheet with id=AC7, first strand: chain 'C' and resid 700 through 701 Processing sheet with id=AC8, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.914A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 748 through 752 removed outlier: 7.233A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 817 through 818 removed outlier: 3.662A pdb=" N GLN C 798 " --> pdb=" O MET C1232 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET C1232 " --> pdb=" O GLN C 798 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 830 through 841 removed outlier: 4.022A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 882 through 884 removed outlier: 7.534A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 887 through 888 removed outlier: 3.567A pdb=" N THR C 888 " --> pdb=" O LYS C 914 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AD6, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.606A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.606A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1251 through 1252 removed outlier: 3.541A pdb=" N TYR C1251 " --> pdb=" O GLU F 114 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1335 through 1339 removed outlier: 3.570A pdb=" N ILE D 20 " --> pdb=" O ASP D1342 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP D1342 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 34 through 37 removed outlier: 4.820A pdb=" N SER D 34 " --> pdb=" O MET D 102 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N HIS D 104 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY D 36 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLU D 106 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 10.542A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.326A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AE3, first strand: chain 'D' and resid 253 through 254 removed outlier: 3.522A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA D 261 " --> pdb=" O VAL D 253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'D' and resid 317 through 319 removed outlier: 4.668A pdb=" N SER D 319 " --> pdb=" O ARG D 322 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 548 through 557 removed outlier: 3.631A pdb=" N THR D 572 " --> pdb=" O VAL D 548 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 809 through 811 removed outlier: 6.647A pdb=" N VAL D 894 " --> pdb=" O VAL D 809 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU D 811 " --> pdb=" O VAL D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.683A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.931A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AF1, first strand: chain 'D' and resid 1002 through 1003 removed outlier: 3.711A pdb=" N VAL D1002 " --> pdb=" O ASN D1019 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1033 through 1034 removed outlier: 4.123A pdb=" N GLY D1033 " --> pdb=" O ILE D1115 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1059 through 1061 removed outlier: 3.788A pdb=" N ALA D1105 " --> pdb=" O VAL D1061 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE D1106 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG D1123 " --> pdb=" O ILE D1106 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1077 through 1079 Processing sheet with id=AF5, first strand: chain 'D' and resid 1176 through 1178 removed outlier: 3.577A pdb=" N GLY D1161 " --> pdb=" O VAL D1204 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL D1204 " --> pdb=" O GLY D1161 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 1280 through 1281 removed outlier: 6.969A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 967 hydrogen bonds defined for protein. 2790 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 76 stacking parallelities Total time for adding SS restraints: 6.82 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8072 1.33 - 1.46: 4868 1.46 - 1.58: 15461 1.58 - 1.70: 198 1.70 - 1.82: 191 Bond restraints: 28790 Sorted by residual: bond pdb=" C1' DC H 32 " pdb=" N1 DC H 32 " ideal model delta sigma weight residual 1.468 1.547 -0.079 1.40e-02 5.10e+03 3.19e+01 bond pdb=" C3' DA G 29 " pdb=" O3' DA G 29 " ideal model delta sigma weight residual 1.435 1.489 -0.054 1.30e-02 5.92e+03 1.72e+01 bond pdb=" C1' DT G 23 " pdb=" N1 DT G 23 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.36e+01 bond pdb=" C3' DG G 3 " pdb=" O3' DG G 3 " ideal model delta sigma weight residual 1.435 1.483 -0.048 1.30e-02 5.92e+03 1.36e+01 bond pdb=" C1' DC H 40 " pdb=" N1 DC H 40 " ideal model delta sigma weight residual 1.468 1.519 -0.051 1.40e-02 5.10e+03 1.33e+01 ... (remaining 28785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 38932 2.84 - 5.69: 350 5.69 - 8.53: 40 8.53 - 11.38: 4 11.38 - 14.22: 2 Bond angle restraints: 39328 Sorted by residual: angle pdb=" O4' DC G 15 " pdb=" C4' DC G 15 " pdb=" C3' DC G 15 " ideal model delta sigma weight residual 106.00 102.88 3.12 6.00e-01 2.78e+00 2.70e+01 angle pdb=" C3' DA H 43 " pdb=" O3' DA H 43 " pdb=" P DT H 44 " ideal model delta sigma weight residual 119.70 125.37 -5.67 1.20e+00 6.94e-01 2.23e+01 angle pdb=" N3 DT H 44 " pdb=" C4 DT H 44 " pdb=" O4 DT H 44 " ideal model delta sigma weight residual 119.90 122.69 -2.79 6.00e-01 2.78e+00 2.17e+01 angle pdb=" N3 DT H 13 " pdb=" C4 DT H 13 " pdb=" O4 DT H 13 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.06e+01 angle pdb=" O5' DG H 14 " pdb=" C5' DG H 14 " pdb=" C4' DG H 14 " ideal model delta sigma weight residual 109.40 113.00 -3.60 8.00e-01 1.56e+00 2.03e+01 ... (remaining 39323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 16873 35.87 - 71.73: 550 71.73 - 107.60: 25 107.60 - 143.46: 2 143.46 - 179.33: 7 Dihedral angle restraints: 17457 sinusoidal: 7837 harmonic: 9620 Sorted by residual: dihedral pdb=" CA ILE D 856 " pdb=" C ILE D 856 " pdb=" N LEU D 857 " pdb=" CA LEU D 857 " ideal model delta harmonic sigma weight residual -180.00 -157.16 -22.84 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ALA D 426 " pdb=" C ALA D 426 " pdb=" N PRO D 427 " pdb=" CA PRO D 427 " ideal model delta harmonic sigma weight residual 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA ASP C 189 " pdb=" C ASP C 189 " pdb=" N PRO C 190 " pdb=" CA PRO C 190 " ideal model delta harmonic sigma weight residual 180.00 157.83 22.17 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 17454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3854 0.073 - 0.145: 591 0.145 - 0.218: 54 0.218 - 0.291: 5 0.291 - 0.363: 2 Chirality restraints: 4506 Sorted by residual: chirality pdb=" CB ILE D 500 " pdb=" CA ILE D 500 " pdb=" CG1 ILE D 500 " pdb=" CG2 ILE D 500 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CB VAL D1027 " pdb=" CA VAL D1027 " pdb=" CG1 VAL D1027 " pdb=" CG2 VAL D1027 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CB VAL D 407 " pdb=" CA VAL D 407 " pdb=" CG1 VAL D 407 " pdb=" CG2 VAL D 407 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 4503 not shown) Planarity restraints: 4793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 856 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.47e+00 pdb=" C ILE D 856 " -0.050 2.00e-02 2.50e+03 pdb=" O ILE D 856 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU D 857 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 850 " -0.042 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO D 851 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 851 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 851 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 501 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO D 502 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO D 502 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 502 " -0.034 5.00e-02 4.00e+02 ... (remaining 4790 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1733 2.74 - 3.28: 24517 3.28 - 3.82: 44541 3.82 - 4.36: 50421 4.36 - 4.90: 86384 Nonbonded interactions: 207596 Sorted by model distance: nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1501 " model vdw 2.197 2.170 nonbonded pdb=" OG SER C 576 " pdb=" O GLN C 659 " model vdw 2.303 3.040 nonbonded pdb=" OG SER C 646 " pdb=" OD1 ASP C 648 " model vdw 2.307 3.040 nonbonded pdb=" O SER D 191 " pdb=" OG SER D 191 " model vdw 2.322 3.040 nonbonded pdb=" O LYS C 476 " pdb=" OG SER C 480 " model vdw 2.331 3.040 ... (remaining 207591 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 138 or (resid 139 and (name N or name CA or name \ C or name O or name CB )) or resid 140 through 232)) selection = (chain 'B' and (resid 8 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 through 135 or (resid 136 and (name N or \ name CA or name C or name O or name CB )) or resid 137 through 158 or resid 170 \ through 232)) } 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: 0.580 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 30.580 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.599 28798 Z= 0.312 Angle : 0.830 41.182 39340 Z= 0.472 Chirality : 0.051 0.363 4506 Planarity : 0.006 0.064 4793 Dihedral : 16.488 179.326 11265 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.06 % Rotamer: Outliers : 0.39 % Allowed : 5.91 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.13 (0.11), residues: 3325 helix: -3.01 (0.09), residues: 1135 sheet: -1.43 (0.23), residues: 396 loop : -2.92 (0.11), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 259 TYR 0.011 0.001 TYR D 631 PHE 0.016 0.001 PHE D1325 TRP 0.009 0.001 TRP D1193 HIS 0.007 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.27 (28790) covalent geometry : angle 0.73044 / 0.47 (39328) hydrogen bonds : bond 0.18296 / 12.28 ( 1026) hydrogen bonds : angle 7.02614 / 4.87 ( 2928) metal coordination : bond 0.26739 / 14.43 ( 8) metal coordination : angle 22.54196 / 12.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 721 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 VAL cc_start: 0.8384 (t) cc_final: 0.8139 (p) REVERT: A 177 TYR cc_start: 0.7413 (m-80) cc_final: 0.6846 (m-10) REVERT: B 16 ILE cc_start: 0.8782 (mt) cc_final: 0.8476 (pt) REVERT: B 147 GLN cc_start: 0.8540 (pt0) cc_final: 0.7401 (pt0) REVERT: C 85 CYS cc_start: 0.8263 (m) cc_final: 0.8042 (t) REVERT: C 156 PHE cc_start: 0.8281 (m-80) cc_final: 0.8078 (m-10) REVERT: C 439 LYS cc_start: 0.7702 (ptpt) cc_final: 0.7303 (pptt) REVERT: C 488 MET cc_start: 0.7716 (tpp) cc_final: 0.7234 (tpt) REVERT: C 654 ASP cc_start: 0.6790 (t0) cc_final: 0.6542 (t0) REVERT: C 768 MET cc_start: 0.8364 (mtp) cc_final: 0.8029 (mtm) REVERT: C 785 ASP cc_start: 0.7867 (m-30) cc_final: 0.7125 (p0) REVERT: C 808 ASN cc_start: 0.8949 (m110) cc_final: 0.8712 (m-40) REVERT: C 949 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6733 (mm-30) REVERT: C 1080 ASN cc_start: 0.8411 (m-40) cc_final: 0.7878 (m-40) REVERT: C 1088 ASP cc_start: 0.8138 (p0) cc_final: 0.7832 (p0) REVERT: C 1230 MET cc_start: 0.8713 (ttm) cc_final: 0.8489 (ttt) REVERT: C 1273 MET cc_start: 0.7850 (mtp) cc_final: 0.7643 (mtm) REVERT: C 1274 GLU cc_start: 0.7859 (mp0) cc_final: 0.7554 (mp0) REVERT: D 527 LEU cc_start: 0.8324 (mm) cc_final: 0.8026 (mm) REVERT: D 872 LEU cc_start: 0.8077 (tt) cc_final: 0.7832 (tt) REVERT: D 1196 LEU cc_start: 0.7688 (mm) cc_final: 0.7437 (mm) REVERT: D 1302 TYR cc_start: 0.8048 (p90) cc_final: 0.7819 (p90) REVERT: D 1327 GLU cc_start: 0.8005 (tt0) cc_final: 0.7763 (tt0) REVERT: F 20 LYS cc_start: 0.8369 (mttp) cc_final: 0.7927 (tptt) REVERT: F 77 ILE cc_start: 0.8905 (mt) cc_final: 0.8636 (tp) REVERT: F 99 ASP cc_start: 0.8556 (t0) cc_final: 0.8019 (t70) REVERT: F 101 ILE cc_start: 0.8656 (mt) cc_final: 0.8251 (mp) outliers start: 11 outliers final: 4 residues processed: 730 average time/residue: 0.2143 time to fit residues: 238.5057 Evaluate side-chains 402 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 398 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 132 HIS A 227 GLN B 132 HIS B 147 GLN C 150 HIS ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS C1157 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN D 450 HIS D 702 GLN D 739 GLN D 817 HIS D 954 ASN D1044 GLN D1114 GLN D1289 ASN E 43 ASN F 105 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.151289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.124173 restraints weight = 47777.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.122391 restraints weight = 63469.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123532 restraints weight = 58406.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.124217 restraints weight = 41894.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.124611 restraints weight = 36519.359| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 28798 Z= 0.217 Angle : 0.672 10.341 39340 Z= 0.351 Chirality : 0.046 0.357 4506 Planarity : 0.005 0.077 4793 Dihedral : 16.475 174.073 4782 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.04 % Allowed : 5.69 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.13), residues: 3325 helix: -0.78 (0.14), residues: 1148 sheet: -1.14 (0.23), residues: 412 loop : -2.48 (0.12), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 515 TYR 0.023 0.001 TYR F 71 PHE 0.025 0.002 PHE C 906 TRP 0.012 0.001 TRP D1193 HIS 0.013 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.22 (28790) covalent geometry : angle 0.66143 / 0.35 (39328) hydrogen bonds : bond 0.04601 / 3.15 ( 1026) hydrogen bonds : angle 4.75846 / 3.34 ( 2928) metal coordination : bond 0.03470 / 1.76 ( 8) metal coordination : angle 6.71201 / 4.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 475 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 ILE cc_start: 0.8869 (mt) cc_final: 0.8621 (pt) REVERT: B 68 TYR cc_start: 0.8959 (m-80) cc_final: 0.8725 (m-80) REVERT: C 347 ILE cc_start: 0.8289 (mm) cc_final: 0.7858 (mm) REVERT: C 369 MET cc_start: 0.6946 (tpt) cc_final: 0.6714 (tpp) REVERT: C 694 ARG cc_start: 0.8174 (ttp-170) cc_final: 0.7439 (ptm160) REVERT: C 768 MET cc_start: 0.8315 (mtp) cc_final: 0.8050 (mtm) REVERT: C 785 ASP cc_start: 0.7783 (m-30) cc_final: 0.7144 (p0) REVERT: C 1088 ASP cc_start: 0.8574 (p0) cc_final: 0.8313 (p0) REVERT: C 1180 MET cc_start: 0.9039 (tpp) cc_final: 0.8408 (ttm) REVERT: C 1274 GLU cc_start: 0.7769 (mp0) cc_final: 0.7333 (mp0) REVERT: D 263 SER cc_start: 0.9491 (m) cc_final: 0.9151 (t) REVERT: D 532 GLU cc_start: 0.8160 (tp30) cc_final: 0.7895 (tp30) REVERT: D 1199 PHE cc_start: 0.6750 (m-10) cc_final: 0.6490 (m-10) REVERT: D 1349 GLU cc_start: 0.7696 (pt0) cc_final: 0.7449 (mt-10) REVERT: F 20 LYS cc_start: 0.8422 (mttp) cc_final: 0.8053 (tptt) REVERT: F 99 ASP cc_start: 0.8543 (t0) cc_final: 0.8222 (t70) outliers start: 1 outliers final: 0 residues processed: 476 average time/residue: 0.1821 time to fit residues: 139.8851 Evaluate side-chains 331 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 262 optimal weight: 4.9990 chunk 326 optimal weight: 9.9990 chunk 328 optimal weight: 0.8980 chunk 111 optimal weight: 0.0370 chunk 269 optimal weight: 0.0000 chunk 67 optimal weight: 50.0000 chunk 252 optimal weight: 4.9990 chunk 228 optimal weight: 0.7980 chunk 270 optimal weight: 20.0000 chunk 190 optimal weight: 5.9990 chunk 312 optimal weight: 8.9990 overall best weight: 1.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN B 23 HIS ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 227 GLN C 649 GLN C 760 ASN ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1220 GLN C1268 GLN D 495 ASN D 739 GLN D 777 HIS ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.151508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.123913 restraints weight = 47220.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.122140 restraints weight = 62120.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123398 restraints weight = 56074.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.123921 restraints weight = 39706.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.124160 restraints weight = 35713.789| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28798 Z= 0.120 Angle : 0.566 8.663 39340 Z= 0.296 Chirality : 0.044 0.358 4506 Planarity : 0.004 0.079 4793 Dihedral : 16.425 173.373 4782 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.13), residues: 3325 helix: 0.13 (0.15), residues: 1150 sheet: -0.91 (0.24), residues: 420 loop : -2.24 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1174 TYR 0.023 0.001 TYR C 70 PHE 0.017 0.001 PHE C 645 TRP 0.016 0.001 TRP D1193 HIS 0.007 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (28790) covalent geometry : angle 0.55716 / 0.30 (39328) hydrogen bonds : bond 0.03681 / 2.51 ( 1026) hydrogen bonds : angle 4.38956 / 3.07 ( 2928) metal coordination : bond 0.00620 / 0.31 ( 8) metal coordination : angle 5.64810 / 3.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.7984 (mmm) cc_final: 0.7756 (tpt) REVERT: C 8 LYS cc_start: 0.8566 (mttt) cc_final: 0.8173 (ttmm) REVERT: C 347 ILE cc_start: 0.8354 (mm) cc_final: 0.7861 (mm) REVERT: C 369 MET cc_start: 0.7170 (tpt) cc_final: 0.6900 (tpp) REVERT: C 468 LEU cc_start: 0.9240 (tp) cc_final: 0.8979 (tp) REVERT: C 559 CYS cc_start: 0.9453 (t) cc_final: 0.9161 (t) REVERT: C 694 ARG cc_start: 0.8266 (ttp-170) cc_final: 0.7547 (ptm160) REVERT: C 768 MET cc_start: 0.8223 (mtp) cc_final: 0.7943 (mtm) REVERT: C 785 ASP cc_start: 0.7786 (m-30) cc_final: 0.7050 (p0) REVERT: C 1088 ASP cc_start: 0.8518 (p0) cc_final: 0.8296 (p0) REVERT: C 1274 GLU cc_start: 0.7723 (mp0) cc_final: 0.7345 (mt-10) REVERT: D 263 SER cc_start: 0.9465 (m) cc_final: 0.9184 (t) REVERT: D 457 TYR cc_start: 0.8755 (m-80) cc_final: 0.8394 (m-80) REVERT: D 532 GLU cc_start: 0.8073 (tp30) cc_final: 0.7872 (tp30) REVERT: D 1196 LEU cc_start: 0.7809 (mm) cc_final: 0.7490 (mm) REVERT: D 1199 PHE cc_start: 0.6749 (m-10) cc_final: 0.6392 (m-10) REVERT: F 20 LYS cc_start: 0.8405 (mttp) cc_final: 0.8019 (tptt) REVERT: F 99 ASP cc_start: 0.8582 (t0) cc_final: 0.8331 (t0) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.1872 time to fit residues: 131.0065 Evaluate side-chains 321 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 89 optimal weight: 8.9990 chunk 167 optimal weight: 7.9990 chunk 269 optimal weight: 20.0000 chunk 236 optimal weight: 0.4980 chunk 169 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 241 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 284 optimal weight: 7.9990 chunk 228 optimal weight: 7.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 HIS ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 227 GLN C 513 GLN C 649 GLN C1090 ASN D 477 GLN D 545 HIS D 777 HIS D 907 HIS ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN F 186 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.147078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.118871 restraints weight = 47592.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.117662 restraints weight = 63385.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.118458 restraints weight = 65315.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.119200 restraints weight = 42936.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119530 restraints weight = 37495.769| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 28798 Z= 0.204 Angle : 0.636 9.740 39340 Z= 0.332 Chirality : 0.046 0.357 4506 Planarity : 0.004 0.076 4793 Dihedral : 16.458 173.025 4782 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.04 % Allowed : 4.28 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.14), residues: 3325 helix: 0.62 (0.15), residues: 1156 sheet: -0.93 (0.24), residues: 431 loop : -2.14 (0.13), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 838 TYR 0.039 0.002 TYR D1186 PHE 0.018 0.002 PHE C 514 TRP 0.017 0.001 TRP D1193 HIS 0.006 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (28790) covalent geometry : angle 0.62924 / 0.33 (39328) hydrogen bonds : bond 0.03988 / 2.72 ( 1026) hydrogen bonds : angle 4.29818 / 3.02 ( 2928) metal coordination : bond 0.01082 / 0.58 ( 8) metal coordination : angle 5.16559 / 3.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 408 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 LYS cc_start: 0.8711 (mttt) cc_final: 0.8153 (ttmm) REVERT: C 295 LYS cc_start: 0.7347 (mmtt) cc_final: 0.7145 (mmtp) REVERT: C 347 ILE cc_start: 0.8250 (mm) cc_final: 0.7635 (mm) REVERT: C 369 MET cc_start: 0.7324 (tpt) cc_final: 0.7087 (tpp) REVERT: C 559 CYS cc_start: 0.9493 (t) cc_final: 0.9176 (t) REVERT: C 694 ARG cc_start: 0.8355 (ttp-170) cc_final: 0.7563 (ptm160) REVERT: C 768 MET cc_start: 0.8203 (mtp) cc_final: 0.7974 (mtm) REVERT: C 785 ASP cc_start: 0.7795 (m-30) cc_final: 0.7153 (p0) REVERT: C 1088 ASP cc_start: 0.8618 (p0) cc_final: 0.8416 (p0) REVERT: C 1274 GLU cc_start: 0.7765 (mp0) cc_final: 0.7501 (mp0) REVERT: D 263 SER cc_start: 0.9646 (m) cc_final: 0.9373 (t) REVERT: D 457 TYR cc_start: 0.8857 (m-80) cc_final: 0.8418 (m-80) REVERT: D 532 GLU cc_start: 0.8219 (tp30) cc_final: 0.7922 (tp30) REVERT: D 872 LEU cc_start: 0.7939 (tp) cc_final: 0.7696 (tp) REVERT: D 1199 PHE cc_start: 0.6605 (m-10) cc_final: 0.6249 (m-10) REVERT: E 18 ASP cc_start: 0.7180 (p0) cc_final: 0.6958 (p0) REVERT: F 20 LYS cc_start: 0.8508 (mttp) cc_final: 0.8031 (tptt) outliers start: 1 outliers final: 0 residues processed: 408 average time/residue: 0.1794 time to fit residues: 118.7985 Evaluate side-chains 305 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 12 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 298 optimal weight: 20.0000 chunk 211 optimal weight: 5.9990 chunk 257 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN C 513 GLN C 649 GLN C1090 ASN ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1299 ASN D 777 HIS D 897 HIS D 907 HIS F 105 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.146155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.118325 restraints weight = 47642.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116130 restraints weight = 69294.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.117237 restraints weight = 60380.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117777 restraints weight = 43832.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.118000 restraints weight = 38690.787| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28798 Z= 0.189 Angle : 0.619 8.238 39340 Z= 0.321 Chirality : 0.046 0.427 4506 Planarity : 0.004 0.080 4793 Dihedral : 16.396 167.358 4782 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.07 % Allowed : 3.15 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.14), residues: 3325 helix: 0.84 (0.16), residues: 1150 sheet: -0.75 (0.25), residues: 434 loop : -2.07 (0.13), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 540 TYR 0.018 0.002 TYR C 346 PHE 0.024 0.002 PHE C1265 TRP 0.013 0.001 TRP D1193 HIS 0.008 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (28790) covalent geometry : angle 0.61347 / 0.32 (39328) hydrogen bonds : bond 0.03843 / 2.61 ( 1026) hydrogen bonds : angle 4.20717 / 2.93 ( 2928) metal coordination : bond 0.00875 / 0.45 ( 8) metal coordination : angle 4.86500 / 2.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 405 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.8472 (tp40) cc_final: 0.8088 (pm20) REVERT: C 8 LYS cc_start: 0.8723 (mttt) cc_final: 0.8228 (ttmm) REVERT: C 132 ASP cc_start: 0.7632 (t0) cc_final: 0.7418 (t0) REVERT: C 347 ILE cc_start: 0.8385 (mm) cc_final: 0.8089 (mm) REVERT: C 369 MET cc_start: 0.7723 (tpt) cc_final: 0.7508 (tpp) REVERT: C 559 CYS cc_start: 0.9556 (t) cc_final: 0.9218 (t) REVERT: C 768 MET cc_start: 0.8242 (mtp) cc_final: 0.8039 (mtm) REVERT: C 785 ASP cc_start: 0.7862 (m-30) cc_final: 0.7126 (p0) REVERT: C 1274 GLU cc_start: 0.7790 (mp0) cc_final: 0.7531 (mp0) REVERT: D 330 MET cc_start: 0.8426 (ttm) cc_final: 0.8146 (ttm) REVERT: D 457 TYR cc_start: 0.8855 (m-80) cc_final: 0.8396 (m-80) REVERT: D 532 GLU cc_start: 0.8228 (tp30) cc_final: 0.7908 (tp30) REVERT: D 1196 LEU cc_start: 0.8131 (mm) cc_final: 0.7678 (mm) REVERT: D 1199 PHE cc_start: 0.6732 (m-10) cc_final: 0.6442 (m-10) REVERT: E 15 ASN cc_start: 0.8236 (t0) cc_final: 0.8009 (t0) REVERT: E 18 ASP cc_start: 0.7304 (p0) cc_final: 0.7018 (p0) REVERT: F 20 LYS cc_start: 0.8538 (mttp) cc_final: 0.7988 (tptt) outliers start: 2 outliers final: 0 residues processed: 405 average time/residue: 0.1760 time to fit residues: 115.1872 Evaluate side-chains 295 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 296 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 240 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 chunk 302 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 chunk 222 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 329 optimal weight: 8.9990 chunk 211 optimal weight: 7.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN C 339 ASN C 513 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 GLN C 686 GLN ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN C1136 GLN C1209 GLN C1299 ASN D 495 ASN D 777 HIS D 907 HIS ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.145295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.117164 restraints weight = 47277.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.115808 restraints weight = 63527.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.117035 restraints weight = 64993.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.117027 restraints weight = 45992.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.118580 restraints weight = 38968.453| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 28798 Z= 0.200 Angle : 0.627 9.304 39340 Z= 0.325 Chirality : 0.045 0.378 4506 Planarity : 0.004 0.083 4793 Dihedral : 16.396 169.037 4782 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.07 % Allowed : 2.23 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.14), residues: 3325 helix: 0.93 (0.16), residues: 1149 sheet: -0.80 (0.25), residues: 434 loop : -1.98 (0.13), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1284 TYR 0.014 0.001 TYR A 177 PHE 0.035 0.002 PHE C 186 TRP 0.010 0.001 TRP D1193 HIS 0.007 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (28790) covalent geometry : angle 0.62158 / 0.32 (39328) hydrogen bonds : bond 0.03890 / 2.63 ( 1026) hydrogen bonds : angle 4.20204 / 2.93 ( 2928) metal coordination : bond 0.01019 / 0.53 ( 8) metal coordination : angle 4.66299 / 2.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 395 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 LYS cc_start: 0.8804 (mttt) cc_final: 0.8193 (ttmm) REVERT: C 132 ASP cc_start: 0.7644 (t0) cc_final: 0.7318 (t0) REVERT: C 347 ILE cc_start: 0.8412 (mm) cc_final: 0.8020 (mm) REVERT: C 524 ILE cc_start: 0.9181 (tt) cc_final: 0.8934 (tt) REVERT: C 559 CYS cc_start: 0.9570 (t) cc_final: 0.9207 (t) REVERT: C 685 MET cc_start: 0.8587 (mtm) cc_final: 0.8264 (mtm) REVERT: C 737 ASN cc_start: 0.8255 (t0) cc_final: 0.8046 (t0) REVERT: C 785 ASP cc_start: 0.7761 (m-30) cc_final: 0.7154 (p0) REVERT: C 1274 GLU cc_start: 0.7805 (mp0) cc_final: 0.7510 (mp0) REVERT: D 457 TYR cc_start: 0.8862 (m-80) cc_final: 0.8438 (m-80) REVERT: D 532 GLU cc_start: 0.8214 (tp30) cc_final: 0.7892 (tp30) REVERT: D 1199 PHE cc_start: 0.6778 (m-10) cc_final: 0.6480 (m-10) REVERT: D 1363 TYR cc_start: 0.8134 (t80) cc_final: 0.7794 (t80) REVERT: E 15 ASN cc_start: 0.8177 (t0) cc_final: 0.7921 (t0) REVERT: E 18 ASP cc_start: 0.7206 (p0) cc_final: 0.6975 (p0) REVERT: F 20 LYS cc_start: 0.8561 (mttp) cc_final: 0.8116 (tptt) outliers start: 2 outliers final: 0 residues processed: 395 average time/residue: 0.1809 time to fit residues: 116.3048 Evaluate side-chains 294 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 223 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 279 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 320 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 203 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 GLN B 147 GLN C 513 GLN C 649 GLN C 686 GLN C1090 ASN ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1299 ASN D 340 GLN D 716 GLN D 777 HIS ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.145439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117550 restraints weight = 47123.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.115840 restraints weight = 65966.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117366 restraints weight = 64175.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117362 restraints weight = 43666.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.118309 restraints weight = 39470.725| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28798 Z= 0.159 Angle : 0.608 12.670 39340 Z= 0.314 Chirality : 0.045 0.377 4506 Planarity : 0.004 0.076 4793 Dihedral : 16.356 168.211 4782 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.11 % Allowed : 1.56 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.14), residues: 3325 helix: 0.99 (0.16), residues: 1152 sheet: -0.71 (0.25), residues: 430 loop : -1.89 (0.13), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 838 TYR 0.012 0.001 TYR D 631 PHE 0.030 0.001 PHE C 186 TRP 0.012 0.001 TRP D1193 HIS 0.007 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (28790) covalent geometry : angle 0.60341 / 0.31 (39328) hydrogen bonds : bond 0.03696 / 2.51 ( 1026) hydrogen bonds : angle 4.13249 / 2.88 ( 2928) metal coordination : bond 0.00851 / 0.44 ( 8) metal coordination : angle 4.14431 / 2.49 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 400 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 LYS cc_start: 0.8818 (mttt) cc_final: 0.8157 (ttmm) REVERT: C 132 ASP cc_start: 0.7643 (t0) cc_final: 0.7330 (t0) REVERT: C 347 ILE cc_start: 0.8418 (mm) cc_final: 0.8041 (mm) REVERT: C 524 ILE cc_start: 0.9140 (tt) cc_final: 0.8884 (tt) REVERT: C 559 CYS cc_start: 0.9591 (t) cc_final: 0.9180 (t) REVERT: C 739 ASP cc_start: 0.8098 (p0) cc_final: 0.7891 (p0) REVERT: C 785 ASP cc_start: 0.7802 (m-30) cc_final: 0.7112 (p0) REVERT: C 1274 GLU cc_start: 0.7790 (mp0) cc_final: 0.7408 (mp0) REVERT: C 1319 MET cc_start: 0.8694 (tpp) cc_final: 0.7961 (ttp) REVERT: D 457 TYR cc_start: 0.8857 (m-80) cc_final: 0.8468 (m-80) REVERT: D 532 GLU cc_start: 0.8247 (tp30) cc_final: 0.7895 (tp30) REVERT: D 1175 LEU cc_start: 0.6415 (tp) cc_final: 0.6172 (tp) REVERT: D 1196 LEU cc_start: 0.8117 (mm) cc_final: 0.7376 (tp) REVERT: D 1199 PHE cc_start: 0.6838 (m-10) cc_final: 0.6558 (m-10) REVERT: D 1349 GLU cc_start: 0.7927 (pt0) cc_final: 0.7635 (mt-10) REVERT: D 1363 TYR cc_start: 0.8147 (t80) cc_final: 0.7852 (t80) REVERT: E 15 ASN cc_start: 0.8175 (t0) cc_final: 0.7871 (t0) REVERT: E 18 ASP cc_start: 0.7261 (p0) cc_final: 0.7058 (p0) REVERT: F 20 LYS cc_start: 0.8560 (mttp) cc_final: 0.8111 (tptt) outliers start: 3 outliers final: 0 residues processed: 400 average time/residue: 0.1781 time to fit residues: 116.3921 Evaluate side-chains 295 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 281 optimal weight: 20.0000 chunk 146 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 302 optimal weight: 0.9980 chunk 231 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 184 optimal weight: 8.9990 chunk 253 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN C 513 GLN C 649 GLN ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN C1146 GLN ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1299 ASN D 777 HIS ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.142451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.114784 restraints weight = 47329.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113470 restraints weight = 62734.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.114251 restraints weight = 70641.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114478 restraints weight = 48295.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.115125 restraints weight = 41711.251| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 28798 Z= 0.228 Angle : 0.676 12.211 39340 Z= 0.346 Chirality : 0.047 0.379 4506 Planarity : 0.005 0.086 4793 Dihedral : 16.419 167.954 4782 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.07 % Allowed : 1.70 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.14), residues: 3325 helix: 0.92 (0.16), residues: 1157 sheet: -0.79 (0.25), residues: 419 loop : -1.89 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 65 TYR 0.019 0.002 TYR C 73 PHE 0.032 0.002 PHE C 514 TRP 0.027 0.002 TRP D1193 HIS 0.008 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.23 (28790) covalent geometry : angle 0.67072 / 0.35 (39328) hydrogen bonds : bond 0.04191 / 2.86 ( 1026) hydrogen bonds : angle 4.25926 / 2.98 ( 2928) metal coordination : bond 0.01200 / 0.62 ( 8) metal coordination : angle 4.76181 / 2.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 371 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 LYS cc_start: 0.8936 (mttt) cc_final: 0.8202 (ttmm) REVERT: C 132 ASP cc_start: 0.7695 (t0) cc_final: 0.7439 (t0) REVERT: C 183 TRP cc_start: 0.8471 (m-10) cc_final: 0.8051 (m-10) REVERT: C 347 ILE cc_start: 0.8523 (mm) cc_final: 0.8120 (mm) REVERT: C 370 MET cc_start: 0.7902 (mmp) cc_final: 0.7602 (mmm) REVERT: C 524 ILE cc_start: 0.9269 (tt) cc_final: 0.9039 (tt) REVERT: C 559 CYS cc_start: 0.9572 (t) cc_final: 0.9223 (t) REVERT: C 785 ASP cc_start: 0.7867 (m-30) cc_final: 0.7165 (p0) REVERT: C 1244 HIS cc_start: 0.7648 (t70) cc_final: 0.7208 (t70) REVERT: C 1274 GLU cc_start: 0.7885 (mp0) cc_final: 0.7513 (mp0) REVERT: C 1319 MET cc_start: 0.8703 (tpp) cc_final: 0.8136 (ttp) REVERT: D 457 TYR cc_start: 0.8866 (m-80) cc_final: 0.8489 (m-80) REVERT: D 532 GLU cc_start: 0.8157 (tp30) cc_final: 0.7915 (tp30) REVERT: D 1196 LEU cc_start: 0.7991 (mm) cc_final: 0.7472 (tp) REVERT: D 1199 PHE cc_start: 0.6814 (m-10) cc_final: 0.6540 (m-10) REVERT: D 1363 TYR cc_start: 0.8192 (t80) cc_final: 0.7950 (t80) REVERT: E 15 ASN cc_start: 0.8314 (t0) cc_final: 0.7959 (t0) REVERT: F 20 LYS cc_start: 0.8598 (mttp) cc_final: 0.8052 (tptt) REVERT: F 23 ASN cc_start: 0.8483 (p0) cc_final: 0.8029 (m-40) outliers start: 2 outliers final: 0 residues processed: 371 average time/residue: 0.1843 time to fit residues: 112.3656 Evaluate side-chains 287 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 69 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 223 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 109 optimal weight: 8.9990 chunk 304 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN C 357 ASN C 513 GLN C 649 GLN C 686 GLN C1090 ASN C1299 ASN D 448 GLN D 777 HIS ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN F 183 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.143927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.115350 restraints weight = 47117.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.113992 restraints weight = 63104.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114892 restraints weight = 63754.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.115468 restraints weight = 43074.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.115724 restraints weight = 38963.317| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28798 Z= 0.167 Angle : 0.627 11.846 39340 Z= 0.322 Chirality : 0.045 0.376 4506 Planarity : 0.004 0.084 4793 Dihedral : 16.367 166.940 4782 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.11 % Allowed : 0.88 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.14), residues: 3325 helix: 1.07 (0.16), residues: 1148 sheet: -0.72 (0.25), residues: 439 loop : -1.78 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1345 TYR 0.025 0.001 TYR A 177 PHE 0.025 0.002 PHE C 186 TRP 0.033 0.001 TRP D1193 HIS 0.006 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (28790) covalent geometry : angle 0.62052 / 0.32 (39328) hydrogen bonds : bond 0.03818 / 2.59 ( 1026) hydrogen bonds : angle 4.19027 / 2.91 ( 2928) metal coordination : bond 0.01064 / 0.55 ( 8) metal coordination : angle 5.32464 / 3.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 376 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 132 ASP cc_start: 0.7725 (t0) cc_final: 0.7397 (t0) REVERT: C 183 TRP cc_start: 0.8419 (m-10) cc_final: 0.8101 (m-10) REVERT: C 347 ILE cc_start: 0.8526 (mm) cc_final: 0.7936 (mm) REVERT: C 370 MET cc_start: 0.7998 (mmp) cc_final: 0.7647 (mmm) REVERT: C 524 ILE cc_start: 0.9130 (tt) cc_final: 0.8891 (tt) REVERT: C 737 ASN cc_start: 0.8388 (t0) cc_final: 0.8115 (t0) REVERT: C 785 ASP cc_start: 0.7892 (m-30) cc_final: 0.7087 (p0) REVERT: C 1274 GLU cc_start: 0.7853 (mp0) cc_final: 0.7419 (mp0) REVERT: C 1319 MET cc_start: 0.8725 (tpp) cc_final: 0.8165 (ttp) REVERT: D 457 TYR cc_start: 0.8819 (m-80) cc_final: 0.8431 (m-80) REVERT: D 532 GLU cc_start: 0.8276 (tp30) cc_final: 0.7922 (tp30) REVERT: D 625 MET cc_start: 0.8562 (ttt) cc_final: 0.8354 (ttt) REVERT: D 1196 LEU cc_start: 0.8036 (mm) cc_final: 0.7538 (tp) REVERT: D 1199 PHE cc_start: 0.6918 (m-10) cc_final: 0.6615 (m-10) REVERT: D 1363 TYR cc_start: 0.8133 (t80) cc_final: 0.7883 (t80) REVERT: E 15 ASN cc_start: 0.8328 (t0) cc_final: 0.7869 (t0) REVERT: F 20 LYS cc_start: 0.8590 (mttp) cc_final: 0.8046 (tptt) REVERT: F 23 ASN cc_start: 0.8563 (p0) cc_final: 0.8103 (m-40) outliers start: 3 outliers final: 2 residues processed: 377 average time/residue: 0.1757 time to fit residues: 109.3301 Evaluate side-chains 290 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 288 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 273 optimal weight: 30.0000 chunk 240 optimal weight: 5.9990 chunk 306 optimal weight: 9.9990 chunk 330 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 327 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 260 optimal weight: 8.9990 chunk 220 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 225 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN C 513 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 GLN C1299 ASN ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.141047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.112958 restraints weight = 47305.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.111466 restraints weight = 66729.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112656 restraints weight = 71132.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.112984 restraints weight = 46906.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.114334 restraints weight = 39990.206| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 28798 Z= 0.265 Angle : 0.724 13.118 39340 Z= 0.370 Chirality : 0.048 0.379 4506 Planarity : 0.005 0.088 4793 Dihedral : 16.457 167.082 4782 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.04 % Allowed : 0.53 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.14), residues: 3325 helix: 0.85 (0.15), residues: 1156 sheet: -0.86 (0.25), residues: 439 loop : -1.87 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 180 TYR 0.021 0.002 TYR A 177 PHE 0.037 0.002 PHE C 514 TRP 0.022 0.002 TRP D1193 HIS 0.009 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.26 (28790) covalent geometry : angle 0.71715 / 0.37 (39328) hydrogen bonds : bond 0.04481 / 3.06 ( 1026) hydrogen bonds : angle 4.39075 / 3.07 ( 2928) metal coordination : bond 0.01391 / 0.71 ( 8) metal coordination : angle 5.79428 / 3.54 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 364 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ARG cc_start: 0.7253 (mtp85) cc_final: 0.7021 (mtt90) REVERT: A 227 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8556 (tt0) REVERT: B 125 LYS cc_start: 0.7679 (tptp) cc_final: 0.7440 (tptt) REVERT: C 132 ASP cc_start: 0.7702 (t0) cc_final: 0.7421 (t0) REVERT: C 183 TRP cc_start: 0.8498 (m-10) cc_final: 0.8074 (m-10) REVERT: C 347 ILE cc_start: 0.8595 (mm) cc_final: 0.7973 (mm) REVERT: C 524 ILE cc_start: 0.9185 (tt) cc_final: 0.8956 (tt) REVERT: C 540 ARG cc_start: 0.8661 (ttp-110) cc_final: 0.8319 (ttp-110) REVERT: C 685 MET cc_start: 0.8579 (mtm) cc_final: 0.8334 (mtp) REVERT: C 737 ASN cc_start: 0.8401 (t0) cc_final: 0.8143 (t0) REVERT: C 785 ASP cc_start: 0.7838 (m-30) cc_final: 0.7128 (p0) REVERT: C 1243 MET cc_start: 0.8614 (ttm) cc_final: 0.8401 (ttm) REVERT: C 1244 HIS cc_start: 0.7655 (t70) cc_final: 0.6990 (t70) REVERT: C 1274 GLU cc_start: 0.7917 (mp0) cc_final: 0.7536 (mp0) REVERT: C 1319 MET cc_start: 0.8745 (tpp) cc_final: 0.8337 (ttp) REVERT: D 457 TYR cc_start: 0.8863 (m-80) cc_final: 0.8531 (m-80) REVERT: D 532 GLU cc_start: 0.8269 (tp30) cc_final: 0.7900 (tp30) REVERT: D 697 MET cc_start: 0.8563 (ttp) cc_final: 0.8213 (ttp) REVERT: D 1196 LEU cc_start: 0.8135 (mm) cc_final: 0.7655 (tp) REVERT: D 1199 PHE cc_start: 0.6965 (m-10) cc_final: 0.6606 (m-10) REVERT: E 15 ASN cc_start: 0.8338 (t0) cc_final: 0.7919 (t0) REVERT: F 20 LYS cc_start: 0.8663 (mttp) cc_final: 0.8063 (tptt) outliers start: 1 outliers final: 0 residues processed: 364 average time/residue: 0.1748 time to fit residues: 105.5677 Evaluate side-chains 288 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 270 optimal weight: 50.0000 chunk 167 optimal weight: 0.9990 chunk 240 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 173 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN C 513 GLN C 649 GLN ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN C1299 ASN D 777 HIS ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.142435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.114719 restraints weight = 47092.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.112764 restraints weight = 67955.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113893 restraints weight = 62140.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.114431 restraints weight = 43335.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.114828 restraints weight = 38586.862| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 28798 Z= 0.195 Angle : 0.660 9.723 39340 Z= 0.339 Chirality : 0.046 0.376 4506 Planarity : 0.004 0.090 4793 Dihedral : 16.428 166.380 4782 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.07 % Allowed : 0.42 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.14), residues: 3325 helix: 0.91 (0.15), residues: 1161 sheet: -0.81 (0.25), residues: 439 loop : -1.86 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 69 TYR 0.022 0.002 TYR C 73 PHE 0.027 0.002 PHE C 514 TRP 0.023 0.001 TRP D1193 HIS 0.006 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (28790) covalent geometry : angle 0.65371 / 0.34 (39328) hydrogen bonds : bond 0.04080 / 2.76 ( 1026) hydrogen bonds : angle 4.28056 / 2.98 ( 2928) metal coordination : bond 0.01094 / 0.57 ( 8) metal coordination : angle 5.27021 / 3.21 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4039.29 seconds wall clock time: 70 minutes 47.92 seconds (4247.92 seconds total)