Starting phenix.real_space_refine on Sun Feb 25 07:03:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7b_23210/02_2024/7l7b_23210_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7b_23210/02_2024/7l7b_23210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7b_23210/02_2024/7l7b_23210.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7b_23210/02_2024/7l7b_23210.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7b_23210/02_2024/7l7b_23210_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7b_23210/02_2024/7l7b_23210_neut_trim_updated.pdb" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.020 sd= 0.120 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 1 5.21 5 S 88 5.16 5 Cl 2 4.86 5 C 15596 2.51 5 N 4256 2.21 5 O 4778 1.98 5 H 25027 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 152": "OE1" <-> "OE2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "B TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C GLU 369": "OE1" <-> "OE2" Residue "C GLU 538": "OE1" <-> "OE2" Residue "C GLU 785": "OE1" <-> "OE2" Residue "C GLU 811": "OE1" <-> "OE2" Residue "C GLU 961": "OE1" <-> "OE2" Residue "C GLU 1107": "OE1" <-> "OE2" Residue "C GLU 1164": "OE1" <-> "OE2" Residue "D GLU 152": "OE1" <-> "OE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D GLU 284": "OE1" <-> "OE2" Residue "D GLU 432": "OE1" <-> "OE2" Residue "D GLU 582": "OE1" <-> "OE2" Residue "D GLU 607": "OE1" <-> "OE2" Residue "D GLU 639": "OE1" <-> "OE2" Residue "D GLU 679": "OE1" <-> "OE2" Residue "D GLU 806": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 49750 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3482 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 212} Chain: "B" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3688 Classifications: {'peptide': 237} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 225} Chain: "C" Number of atoms: 18442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 18442 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 49, 'TRANS': 1116} Chain: "D" Number of atoms: 18266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1148, 18266 Classifications: {'peptide': 1148} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 1101} Chain breaks: 1 Chain: "E" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1279 Classifications: {'peptide': 78} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 74} Chain: "F" Number of atoms: 4487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4487 Classifications: {'peptide': 272} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 258} Chain: "D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 75 Unusual residues: {' MG': 1, ' ZN': 2, 'FI8': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 38253 SG CYS D 790 37.931 98.935 89.757 1.00101.42 S ATOM 39409 SG CYS D 864 40.535 96.539 88.684 1.00100.07 S ATOM 39509 SG CYS D 871 40.214 98.274 91.810 1.00 95.85 S ATOM 39552 SG CYS D 874 37.576 96.119 91.434 1.00100.42 S ATOM 26572 SG CYS D 60 99.102 106.863 64.018 1.00130.49 S ATOM 26599 SG CYS D 62 100.503 106.459 61.132 1.00132.98 S ATOM 26829 SG CYS D 75 99.099 109.502 61.473 1.00136.11 S ATOM 26875 SG CYS D 78 97.250 106.048 60.636 1.00132.03 S Time building chain proxies: 20.39, per 1000 atoms: 0.41 Number of scatterers: 49750 At special positions: 0 Unit cell: (134.292, 134.292, 180.861, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 Cl 2 17.00 S 88 16.00 Mg 1 11.99 O 4778 8.00 N 4256 7.00 C 15596 6.00 H 25027 1.00 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 - 3.50 Amino acid : False - 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: 39.61 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1401 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 874 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 864 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 790 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 871 " pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 78 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " Number of angles added : 12 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5790 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 26 sheets defined 34.5% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.21 Creating SS restraints... Processing helix chain 'A' and resid 32 through 46 removed outlier: 3.910A pdb=" N ILE A 36 " --> pdb=" O TYR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 79 No H-bonds generated for 'chain 'A' and resid 76 through 79' Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 151 through 154 No H-bonds generated for 'chain 'A' and resid 151 through 154' Processing helix chain 'A' and resid 206 through 221 Processing helix chain 'B' and resid 30 through 46 removed outlier: 3.914A pdb=" N GLY B 33 " --> pdb=" O ARG B 30 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE B 34 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR B 35 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ILE B 36 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 46 " --> pdb=" O ILE B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 84 removed outlier: 3.583A pdb=" N ILE B 79 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU B 80 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 222 removed outlier: 3.779A pdb=" N ILE B 210 " --> pdb=" O PRO B 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 50 removed outlier: 3.824A pdb=" N LYS C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE C 50 " --> pdb=" O VAL C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 203 through 213 removed outlier: 3.950A pdb=" N LEU C 210 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU C 212 " --> pdb=" O ASP C 208 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ASP C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 222 Processing helix chain 'C' and resid 228 through 239 Processing helix chain 'C' and resid 247 through 258 removed outlier: 3.768A pdb=" N ASN C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 277 Processing helix chain 'C' and resid 280 through 284 Processing helix chain 'C' and resid 311 through 320 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 354 through 356 No H-bonds generated for 'chain 'C' and resid 354 through 356' Processing helix chain 'C' and resid 364 through 373 Processing helix chain 'C' and resid 377 through 391 removed outlier: 5.479A pdb=" N LYS C 389 " --> pdb=" O LYS C 385 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLU C 390 " --> pdb=" O SER C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 413 removed outlier: 3.771A pdb=" N ILE C 405 " --> pdb=" O ILE C 401 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE C 412 " --> pdb=" O GLU C 408 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR C 413 " --> pdb=" O PHE C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 455 Processing helix chain 'C' and resid 465 through 468 No H-bonds generated for 'chain 'C' and resid 465 through 468' Processing helix chain 'C' and resid 472 through 482 Processing helix chain 'C' and resid 496 through 503 Processing helix chain 'C' and resid 586 through 591 Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 650 through 652 No H-bonds generated for 'chain 'C' and resid 650 through 652' Processing helix chain 'C' and resid 655 through 664 Processing helix chain 'C' and resid 684 through 690 Processing helix chain 'C' and resid 792 through 796 removed outlier: 3.818A pdb=" N LYS C 796 " --> pdb=" O ARG C 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 834 removed outlier: 3.542A pdb=" N ILE C 834 " --> pdb=" O ASP C 831 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 831 through 834' Processing helix chain 'C' and resid 869 through 878 Processing helix chain 'C' and resid 972 through 978 Proline residue: C 976 - end of helix Processing helix chain 'C' and resid 982 through 996 Processing helix chain 'C' and resid 1010 through 1020 Processing helix chain 'C' and resid 1057 through 1059 No H-bonds generated for 'chain 'C' and resid 1057 through 1059' Processing helix chain 'C' and resid 1090 through 1099 Processing helix chain 'C' and resid 1102 through 1110 Processing helix chain 'C' and resid 1116 through 1128 removed outlier: 3.549A pdb=" N GLU C1124 " --> pdb=" O VAL C1120 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA C1125 " --> pdb=" O ARG C1121 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1151 removed outlier: 3.835A pdb=" N LEU C1151 " --> pdb=" O GLU C1147 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 85 through 89 Processing helix chain 'D' and resid 105 through 108 No H-bonds generated for 'chain 'D' and resid 105 through 108' Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 152 through 161 Processing helix chain 'D' and resid 172 through 181 Processing helix chain 'D' and resid 185 through 197 Processing helix chain 'D' and resid 201 through 218 removed outlier: 3.679A pdb=" N VAL D 212 " --> pdb=" O ARG D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 238 No H-bonds generated for 'chain 'D' and resid 236 through 238' Processing helix chain 'D' and resid 254 through 274 Processing helix chain 'D' and resid 278 through 296 Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 376 Processing helix chain 'D' and resid 383 through 391 removed outlier: 3.504A pdb=" N VAL D 390 " --> pdb=" O ALA D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 404 removed outlier: 3.578A pdb=" N ASP D 399 " --> pdb=" O GLU D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 422 No H-bonds generated for 'chain 'D' and resid 420 through 422' Processing helix chain 'D' and resid 441 through 446 removed outlier: 3.891A pdb=" N THR D 444 " --> pdb=" O LEU D 441 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA D 445 " --> pdb=" O VAL D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 472 Processing helix chain 'D' and resid 475 through 477 No H-bonds generated for 'chain 'D' and resid 475 through 477' Processing helix chain 'D' and resid 493 through 501 Processing helix chain 'D' and resid 520 through 528 Processing helix chain 'D' and resid 556 through 562 Processing helix chain 'D' and resid 589 through 602 Processing helix chain 'D' and resid 612 through 626 removed outlier: 3.602A pdb=" N LYS D 616 " --> pdb=" O LEU D 612 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA D 617 " --> pdb=" O ASP D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 660 removed outlier: 4.425A pdb=" N TYR D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 691 Processing helix chain 'D' and resid 697 through 703 Processing helix chain 'D' and resid 710 through 716 Processing helix chain 'D' and resid 745 through 779 removed outlier: 4.585A pdb=" N LYS D 757 " --> pdb=" O HIS D 753 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLY D 758 " --> pdb=" O GLY D 754 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU D 759 " --> pdb=" O ALA D 755 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 760 " --> pdb=" O ARG D 756 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA D 767 " --> pdb=" O ALA D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 850 Processing helix chain 'D' and resid 861 through 863 No H-bonds generated for 'chain 'D' and resid 861 through 863' Processing helix chain 'D' and resid 872 through 875 No H-bonds generated for 'chain 'D' and resid 872 through 875' Processing helix chain 'D' and resid 891 through 901 Processing helix chain 'D' and resid 903 through 907 Processing helix chain 'D' and resid 925 through 932 Processing helix chain 'D' and resid 1004 through 1008 Processing helix chain 'D' and resid 1011 through 1027 Processing helix chain 'D' and resid 1035 through 1045 Processing helix chain 'D' and resid 1067 through 1078 removed outlier: 4.131A pdb=" N ASP D1076 " --> pdb=" O GLU D1072 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA D1077 " --> pdb=" O CYS D1073 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE D1078 " --> pdb=" O ASN D1074 " (cutoff:3.500A) Processing helix chain 'D' and resid 1094 through 1097 No H-bonds generated for 'chain 'D' and resid 1094 through 1097' Processing helix chain 'D' and resid 1104 through 1109 removed outlier: 4.149A pdb=" N SER D1109 " --> pdb=" O LEU D1105 " (cutoff:3.500A) Processing helix chain 'D' and resid 1113 through 1121 Processing helix chain 'D' and resid 1134 through 1138 Processing helix chain 'D' and resid 1145 through 1147 No H-bonds generated for 'chain 'D' and resid 1145 through 1147' Processing helix chain 'D' and resid 1149 through 1152 No H-bonds generated for 'chain 'D' and resid 1149 through 1152' Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 66 through 76 Processing helix chain 'F' and resid 118 through 128 Processing helix chain 'F' and resid 136 through 143 Processing helix chain 'F' and resid 149 through 169 removed outlier: 4.660A pdb=" N ARG F 161 " --> pdb=" O GLU F 157 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU F 162 " --> pdb=" O ALA F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 193 Processing helix chain 'F' and resid 203 through 219 removed outlier: 3.975A pdb=" N THR F 208 " --> pdb=" O SER F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 250 Processing helix chain 'F' and resid 256 through 263 Processing helix chain 'F' and resid 267 through 277 Processing helix chain 'F' and resid 307 through 326 removed outlier: 3.721A pdb=" N SER F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 339 Processing helix chain 'F' and resid 349 through 355 Processing helix chain 'F' and resid 360 through 375 Processing helix chain 'F' and resid 377 through 384 removed outlier: 5.445A pdb=" N LYS F 382 " --> pdb=" O SER F 378 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU F 383 " --> pdb=" O ARG F 379 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 8 through 11 removed outlier: 3.549A pdb=" N LYS A 8 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 26 " --> pdb=" O LYS A 8 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP A 10 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A 24 " --> pdb=" O ASP A 10 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 50 through 53 removed outlier: 3.790A pdb=" N ALA A 52 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP A 143 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 56 through 58 removed outlier: 3.502A pdb=" N GLU A 139 " --> pdb=" O LYS A 57 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 8 through 10 Processing sheet with id= E, first strand: chain 'B' and resid 95 through 102 removed outlier: 3.861A pdb=" N ALA B 55 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ASP B 143 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL B 53 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLY B 145 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL B 51 " --> pdb=" O GLY B 145 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 105 through 107 removed outlier: 3.977A pdb=" N ALA B 128 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.557A pdb=" N HIS C 3 " --> pdb=" O SER C 14 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER C 14 " --> pdb=" O HIS C 3 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 60 through 63 Processing sheet with id= I, first strand: chain 'C' and resid 124 through 126 Processing sheet with id= J, first strand: chain 'C' and resid 142 through 145 removed outlier: 4.183A pdb=" N ILE C 162 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 169 through 173 removed outlier: 4.025A pdb=" N GLU C 170 " --> pdb=" O ARG C 182 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 324 through 328 Processing sheet with id= M, first strand: chain 'C' and resid 505 through 507 Processing sheet with id= N, first strand: chain 'C' and resid 581 through 584 Processing sheet with id= O, first strand: chain 'C' and resid 612 through 614 Processing sheet with id= P, first strand: chain 'C' and resid 720 through 724 removed outlier: 6.188A pdb=" N LYS C 714 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ALA C 703 " --> pdb=" O LYS C 714 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 770 through 775 Processing sheet with id= R, first strand: chain 'C' and resid 803 through 810 removed outlier: 3.856A pdb=" N VAL C 922 " --> pdb=" O CYS C 810 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 859 through 861 Processing sheet with id= T, first strand: chain 'C' and resid 88 through 92 removed outlier: 4.059A pdb=" N GLY C 113 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 241 through 244 removed outlier: 3.728A pdb=" N LEU D 244 " --> pdb=" O ARG D 248 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG D 248 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 454 through 456 removed outlier: 3.551A pdb=" N VAL D 345 " --> pdb=" O ILE D 436 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 354 through 358 removed outlier: 7.635A pdb=" N CYS D 355 " --> pdb=" O ALA D 425 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLU D 427 " --> pdb=" O CYS D 355 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU D 357 " --> pdb=" O GLU D 427 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE D 429 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE D 426 " --> pdb=" O VAL D 410 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 537 through 543 Processing sheet with id= Y, first strand: chain 'D' and resid 796 through 798 removed outlier: 3.869A pdb=" N ILE D 856 " --> pdb=" O ILE D 798 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 949 through 951 739 hydrogen bonds defined for protein. 2067 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.58 Time building geometry restraints manager: 40.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 25005 1.02 - 1.22: 46 1.22 - 1.42: 9961 1.42 - 1.62: 14945 1.62 - 1.83: 149 Bond restraints: 50106 Sorted by residual: bond pdb=" C LEU D 418 " pdb=" O LEU D 418 " ideal model delta sigma weight residual 1.237 1.106 0.130 1.17e-02 7.31e+03 1.24e+02 bond pdb=" C PRO D 416 " pdb=" O PRO D 416 " ideal model delta sigma weight residual 1.235 1.157 0.078 7.90e-03 1.60e+04 9.69e+01 bond pdb=" C HIS D 419 " pdb=" O HIS D 419 " ideal model delta sigma weight residual 1.235 1.128 0.107 1.26e-02 6.30e+03 7.18e+01 bond pdb=" CA LEU D 418 " pdb=" C LEU D 418 " ideal model delta sigma weight residual 1.523 1.414 0.109 1.30e-02 5.92e+03 7.01e+01 bond pdb=" C VAL C1143 " pdb=" N LEU C1144 " ideal model delta sigma weight residual 1.335 1.231 0.104 1.31e-02 5.83e+03 6.30e+01 ... (remaining 50101 not shown) Histogram of bond angle deviations from ideal: 98.45 - 105.57: 497 105.57 - 112.68: 60220 112.68 - 119.79: 13128 119.79 - 126.90: 16980 126.90 - 134.02: 233 Bond angle restraints: 91058 Sorted by residual: angle pdb=" CA PRO D 416 " pdb=" C PRO D 416 " pdb=" N THR D 417 " ideal model delta sigma weight residual 116.09 125.28 -9.19 9.20e-01 1.18e+00 9.97e+01 angle pdb=" CA PRO D 416 " pdb=" C PRO D 416 " pdb=" O PRO D 416 " ideal model delta sigma weight residual 121.11 110.57 10.54 1.08e+00 8.57e-01 9.53e+01 angle pdb=" CA ALA D 415 " pdb=" C ALA D 415 " pdb=" N PRO D 416 " ideal model delta sigma weight residual 120.52 126.55 -6.03 8.30e-01 1.45e+00 5.27e+01 angle pdb=" CA LEU D 418 " pdb=" C LEU D 418 " pdb=" O LEU D 418 " ideal model delta sigma weight residual 120.55 113.33 7.22 1.06e+00 8.90e-01 4.64e+01 angle pdb=" C SER C 51 " pdb=" N PRO C 52 " pdb=" CA PRO C 52 " ideal model delta sigma weight residual 119.76 113.55 6.21 1.00e+00 1.00e+00 3.85e+01 ... (remaining 91053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.38: 22507 31.38 - 62.76: 719 62.76 - 94.14: 23 94.14 - 125.52: 1 125.52 - 156.90: 4 Dihedral angle restraints: 23254 sinusoidal: 13194 harmonic: 10060 Sorted by residual: dihedral pdb=" CA GLU D 582 " pdb=" C GLU D 582 " pdb=" N VAL D 583 " pdb=" CA VAL D 583 " ideal model delta harmonic sigma weight residual 180.00 150.86 29.14 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA GLN B 187 " pdb=" C GLN B 187 " pdb=" N LYS B 188 " pdb=" CA LYS B 188 " ideal model delta harmonic sigma weight residual -180.00 -151.35 -28.65 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA GLU D 505 " pdb=" C GLU D 505 " pdb=" N ALA D 506 " pdb=" CA ALA D 506 " ideal model delta harmonic sigma weight residual 180.00 154.49 25.51 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 23251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 3846 0.142 - 0.284: 18 0.284 - 0.426: 3 0.426 - 0.567: 2 0.567 - 0.709: 1 Chirality restraints: 3870 Sorted by residual: chirality pdb=" CA HIS D 419 " pdb=" N HIS D 419 " pdb=" C HIS D 419 " pdb=" CB HIS D 419 " both_signs ideal model delta sigma weight residual False 2.51 1.80 0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CB THR D 417 " pdb=" CA THR D 417 " pdb=" OG1 THR D 417 " pdb=" CG2 THR D 417 " both_signs ideal model delta sigma weight residual False 2.55 2.05 0.50 2.00e-01 2.50e+01 6.21e+00 chirality pdb=" CA LEU D 418 " pdb=" N LEU D 418 " pdb=" C LEU D 418 " pdb=" CB LEU D 418 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.03e+00 ... (remaining 3867 not shown) Planarity restraints: 7383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP D 453 " -0.045 2.00e-02 2.50e+03 8.84e-02 7.81e+01 pdb=" CG ASP D 453 " 0.153 2.00e-02 2.50e+03 pdb=" OD1 ASP D 453 " -0.059 2.00e-02 2.50e+03 pdb=" OD2 ASP D 453 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 401 " -0.033 2.00e-02 2.50e+03 6.32e-02 4.00e+01 pdb=" N ILE C 402 " 0.109 2.00e-02 2.50e+03 pdb=" CA ILE C 402 " -0.027 2.00e-02 2.50e+03 pdb=" H ILE C 402 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 413 " -0.030 2.00e-02 2.50e+03 6.04e-02 3.65e+01 pdb=" C ASN D 413 " 0.104 2.00e-02 2.50e+03 pdb=" O ASN D 413 " -0.040 2.00e-02 2.50e+03 pdb=" N ARG D 414 " -0.035 2.00e-02 2.50e+03 ... (remaining 7380 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 851 2.10 - 2.72: 87543 2.72 - 3.35: 141502 3.35 - 3.97: 174199 3.97 - 4.60: 280525 Nonbonded interactions: 684620 Sorted by model distance: nonbonded pdb=" H THR E 65 " pdb=" OE2 GLU E 68 " model vdw 1.472 1.850 nonbonded pdb=" OE2 GLU C 291 " pdb="HD21 ASN C 326 " model vdw 1.500 1.850 nonbonded pdb="HD22 ASN C 744 " pdb=" OD2 ASP C 747 " model vdw 1.504 1.850 nonbonded pdb=" HH TYR C1069 " pdb=" OD2 ASP D 337 " model vdw 1.538 1.850 nonbonded pdb=" HG SER D1103 " pdb=" OE2 GLU D1134 " model vdw 1.540 1.850 ... (remaining 684615 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3)) or resid 6 through 228)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.800 Extract box with map and model: 6.890 Check model and map are aligned: 0.780 Set scattering table: 0.470 Process input model: 165.270 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.233 25079 Z= 0.332 Angle : 0.717 12.369 33874 Z= 0.411 Chirality : 0.048 0.709 3870 Planarity : 0.005 0.088 4398 Dihedral : 12.892 156.896 9728 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.78 % Favored : 93.19 % Rotamer: Outliers : 0.22 % Allowed : 0.52 % Favored : 99.26 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.15), residues: 3111 helix: 0.71 (0.16), residues: 1087 sheet: -2.04 (0.29), residues: 309 loop : -1.78 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 998 HIS 0.022 0.001 HIS D 419 PHE 0.019 0.001 PHE D 579 TYR 0.036 0.001 TYR F 197 ARG 0.003 0.000 ARG C 872 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 244 time to evaluate : 4.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 LYS cc_start: 0.8966 (tttp) cc_final: 0.8620 (ttpp) REVERT: B 92 GLU cc_start: 0.7568 (tp30) cc_final: 0.7226 (tp30) REVERT: C 36 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7411 (tm-30) REVERT: C 380 ILE cc_start: 0.7976 (mt) cc_final: 0.7531 (tp) REVERT: C 414 ASN cc_start: 0.8630 (m-40) cc_final: 0.8419 (p0) REVERT: C 480 GLU cc_start: 0.8253 (tm-30) cc_final: 0.8036 (tp30) REVERT: C 1006 ASP cc_start: 0.8052 (t0) cc_final: 0.7784 (t0) REVERT: C 1147 GLU cc_start: 0.7762 (tp30) cc_final: 0.7536 (tp30) REVERT: D 59 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7327 (tm-30) REVERT: D 319 MET cc_start: 0.8280 (mtp) cc_final: 0.8049 (mtp) REVERT: D 701 MET cc_start: 0.7644 (mtp) cc_final: 0.7301 (mtp) REVERT: D 867 ASN cc_start: 0.8503 (m110) cc_final: 0.8296 (m-40) REVERT: F 144 MET cc_start: 0.7832 (mmp) cc_final: 0.7456 (mmm) REVERT: F 170 TYR cc_start: 0.6947 (m-10) cc_final: 0.6732 (m-10) REVERT: F 263 MET cc_start: 0.6506 (ttm) cc_final: 0.6236 (ttp) REVERT: F 324 LEU cc_start: 0.7380 (tp) cc_final: 0.7031 (tt) outliers start: 6 outliers final: 3 residues processed: 249 average time/residue: 0.8964 time to fit residues: 345.0533 Evaluate side-chains 193 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 190 time to evaluate : 3.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1143 VAL Chi-restraints excluded: chain D residue 579 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 4.9990 chunk 234 optimal weight: 0.1980 chunk 129 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 280 optimal weight: 2.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25079 Z= 0.260 Angle : 0.543 5.843 33874 Z= 0.285 Chirality : 0.042 0.150 3870 Planarity : 0.004 0.083 4398 Dihedral : 6.890 142.403 3507 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.71 % Favored : 92.25 % Rotamer: Outliers : 0.78 % Allowed : 4.40 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.15), residues: 3111 helix: 0.78 (0.16), residues: 1090 sheet: -2.08 (0.28), residues: 338 loop : -1.77 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 998 HIS 0.007 0.001 HIS D 419 PHE 0.017 0.001 PHE D 166 TYR 0.013 0.001 TYR D 622 ARG 0.004 0.000 ARG D 286 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 200 time to evaluate : 4.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 LYS cc_start: 0.8969 (tttp) cc_final: 0.8616 (ttpp) REVERT: B 92 GLU cc_start: 0.7610 (tp30) cc_final: 0.7180 (tp30) REVERT: C 36 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7482 (tm-30) REVERT: C 112 MET cc_start: 0.8280 (tpp) cc_final: 0.8031 (tpp) REVERT: C 380 ILE cc_start: 0.8078 (mt) cc_final: 0.7676 (tp) REVERT: C 480 GLU cc_start: 0.8256 (tm-30) cc_final: 0.8030 (tp30) REVERT: C 1147 GLU cc_start: 0.7874 (tp30) cc_final: 0.7576 (tp30) REVERT: D 319 MET cc_start: 0.8403 (mtp) cc_final: 0.8088 (mtp) REVERT: D 867 ASN cc_start: 0.8542 (m110) cc_final: 0.8338 (m-40) REVERT: E 72 GLU cc_start: 0.7708 (tp30) cc_final: 0.7194 (tm-30) REVERT: F 263 MET cc_start: 0.6560 (ttm) cc_final: 0.6303 (ttp) REVERT: F 284 GLU cc_start: 0.7706 (mp0) cc_final: 0.7108 (mp0) REVERT: F 324 LEU cc_start: 0.7281 (tp) cc_final: 0.7028 (tt) outliers start: 21 outliers final: 14 residues processed: 216 average time/residue: 0.9385 time to fit residues: 316.2120 Evaluate side-chains 198 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 4.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 596 GLN Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1150 SER Chi-restraints excluded: chain D residue 553 GLU Chi-restraints excluded: chain D residue 973 TYR Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain F residue 282 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 233 optimal weight: 0.2980 chunk 191 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 281 optimal weight: 2.9990 chunk 303 optimal weight: 8.9990 chunk 250 optimal weight: 2.9990 chunk 278 optimal weight: 0.1980 chunk 95 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 ASN ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25079 Z= 0.196 Angle : 0.511 5.831 33874 Z= 0.267 Chirality : 0.041 0.147 3870 Planarity : 0.004 0.076 4398 Dihedral : 6.316 144.420 3504 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.39 % Favored : 92.57 % Rotamer: Outliers : 0.48 % Allowed : 6.14 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.15), residues: 3111 helix: 0.86 (0.16), residues: 1095 sheet: -1.86 (0.29), residues: 320 loop : -1.77 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 998 HIS 0.006 0.001 HIS E 76 PHE 0.019 0.001 PHE D 166 TYR 0.012 0.001 TYR C 145 ARG 0.002 0.000 ARG C1064 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 197 time to evaluate : 4.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 LYS cc_start: 0.8957 (tttp) cc_final: 0.8620 (ttpp) REVERT: B 92 GLU cc_start: 0.7584 (tp30) cc_final: 0.7154 (tp30) REVERT: C 36 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7438 (tm-30) REVERT: C 480 GLU cc_start: 0.8261 (tm-30) cc_final: 0.8032 (tp30) REVERT: C 1147 GLU cc_start: 0.7787 (tp30) cc_final: 0.7571 (tp30) REVERT: D 59 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7273 (tm-30) REVERT: D 319 MET cc_start: 0.8428 (mtp) cc_final: 0.8103 (mtp) REVERT: D 867 ASN cc_start: 0.8533 (m110) cc_final: 0.8330 (m-40) REVERT: F 284 GLU cc_start: 0.7716 (mp0) cc_final: 0.7110 (mp0) REVERT: F 324 LEU cc_start: 0.7268 (tp) cc_final: 0.7015 (tt) outliers start: 13 outliers final: 11 residues processed: 208 average time/residue: 0.9590 time to fit residues: 304.3589 Evaluate side-chains 198 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 187 time to evaluate : 4.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1150 SER Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 553 GLU Chi-restraints excluded: chain D residue 973 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 188 optimal weight: 0.0770 chunk 282 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 267 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN D 715 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25079 Z= 0.259 Angle : 0.526 6.075 33874 Z= 0.275 Chirality : 0.042 0.145 3870 Planarity : 0.004 0.071 4398 Dihedral : 6.162 144.257 3504 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.49 % Favored : 91.48 % Rotamer: Outliers : 0.67 % Allowed : 7.66 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.15), residues: 3111 helix: 0.85 (0.16), residues: 1092 sheet: -2.03 (0.28), residues: 338 loop : -1.79 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 998 HIS 0.006 0.001 HIS E 76 PHE 0.018 0.001 PHE D 166 TYR 0.014 0.001 TYR D 622 ARG 0.007 0.000 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 192 time to evaluate : 4.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 GLU cc_start: 0.7611 (tp30) cc_final: 0.7157 (tp30) REVERT: B 237 MET cc_start: 0.8287 (mmm) cc_final: 0.8078 (mmm) REVERT: C 36 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7417 (tm-30) REVERT: C 380 ILE cc_start: 0.8139 (mt) cc_final: 0.7586 (tp) REVERT: C 480 GLU cc_start: 0.8292 (tm-30) cc_final: 0.8046 (tp30) REVERT: D 319 MET cc_start: 0.8455 (mtp) cc_final: 0.8198 (mtp) REVERT: D 867 ASN cc_start: 0.8542 (m110) cc_final: 0.8338 (m-40) REVERT: F 284 GLU cc_start: 0.7670 (mp0) cc_final: 0.7096 (mp0) REVERT: F 324 LEU cc_start: 0.7268 (tp) cc_final: 0.7001 (tt) outliers start: 18 outliers final: 13 residues processed: 205 average time/residue: 0.9812 time to fit residues: 308.3577 Evaluate side-chains 196 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 183 time to evaluate : 4.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1150 SER Chi-restraints excluded: chain D residue 553 GLU Chi-restraints excluded: chain D residue 973 TYR Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain F residue 282 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 254 optimal weight: 5.9990 chunk 206 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 268 optimal weight: 0.5980 chunk 75 optimal weight: 20.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 ASN ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25079 Z= 0.206 Angle : 0.504 5.571 33874 Z= 0.263 Chirality : 0.041 0.146 3870 Planarity : 0.004 0.068 4398 Dihedral : 6.034 143.392 3504 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.10 % Favored : 92.86 % Rotamer: Outliers : 0.59 % Allowed : 8.77 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.15), residues: 3111 helix: 0.94 (0.16), residues: 1090 sheet: -1.85 (0.28), residues: 327 loop : -1.75 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 998 HIS 0.007 0.001 HIS E 76 PHE 0.020 0.001 PHE D 166 TYR 0.011 0.001 TYR D 622 ARG 0.005 0.000 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 194 time to evaluate : 4.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 GLU cc_start: 0.7638 (tp30) cc_final: 0.7369 (tp30) REVERT: C 36 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7405 (tm-30) REVERT: C 380 ILE cc_start: 0.8197 (mt) cc_final: 0.7708 (tp) REVERT: C 480 GLU cc_start: 0.8274 (tm-30) cc_final: 0.8027 (tp30) REVERT: D 661 ARG cc_start: 0.7809 (ptm-80) cc_final: 0.7487 (ptt90) REVERT: D 867 ASN cc_start: 0.8539 (m110) cc_final: 0.8327 (m-40) REVERT: F 284 GLU cc_start: 0.7595 (mp0) cc_final: 0.7138 (mp0) REVERT: F 324 LEU cc_start: 0.7234 (tp) cc_final: 0.6980 (tt) outliers start: 16 outliers final: 12 residues processed: 206 average time/residue: 0.9948 time to fit residues: 315.3973 Evaluate side-chains 198 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 186 time to evaluate : 4.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1150 SER Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 973 TYR Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 282 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 3.9990 chunk 268 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 298 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 GLN ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25079 Z= 0.321 Angle : 0.541 5.530 33874 Z= 0.285 Chirality : 0.043 0.150 3870 Planarity : 0.004 0.066 4398 Dihedral : 6.155 143.329 3504 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.13 % Favored : 90.81 % Rotamer: Outliers : 1.00 % Allowed : 9.14 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.15), residues: 3111 helix: 0.83 (0.16), residues: 1089 sheet: -2.02 (0.28), residues: 340 loop : -1.82 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 998 HIS 0.006 0.001 HIS E 76 PHE 0.020 0.001 PHE D 166 TYR 0.016 0.001 TYR D 622 ARG 0.005 0.000 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 192 time to evaluate : 4.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7625 (pt) REVERT: B 92 GLU cc_start: 0.7651 (tp30) cc_final: 0.7378 (tp30) REVERT: C 36 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7419 (tm-30) REVERT: C 380 ILE cc_start: 0.8205 (mt) cc_final: 0.7751 (tp) REVERT: C 480 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8062 (tp30) REVERT: D 83 THR cc_start: 0.8851 (t) cc_final: 0.8624 (m) REVERT: D 319 MET cc_start: 0.8419 (mtp) cc_final: 0.8127 (mtp) REVERT: D 661 ARG cc_start: 0.7767 (ptm-80) cc_final: 0.7480 (ptt90) REVERT: D 867 ASN cc_start: 0.8542 (m110) cc_final: 0.8328 (m-40) REVERT: E 73 GLU cc_start: 0.6328 (mm-30) cc_final: 0.6063 (mm-30) REVERT: F 278 GLN cc_start: 0.7990 (mt0) cc_final: 0.7626 (mt0) REVERT: F 284 GLU cc_start: 0.7586 (mp0) cc_final: 0.7076 (mp0) REVERT: F 324 LEU cc_start: 0.7220 (tp) cc_final: 0.6975 (tt) outliers start: 27 outliers final: 18 residues processed: 214 average time/residue: 0.9992 time to fit residues: 331.2152 Evaluate side-chains 205 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 186 time to evaluate : 4.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1150 SER Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 553 GLU Chi-restraints excluded: chain D residue 579 PHE Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 907 THR Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain F residue 282 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 218 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 251 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 297 optimal weight: 7.9990 chunk 186 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25079 Z= 0.240 Angle : 0.514 6.011 33874 Z= 0.269 Chirality : 0.042 0.146 3870 Planarity : 0.004 0.065 4398 Dihedral : 6.045 143.112 3503 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.59 % Favored : 92.38 % Rotamer: Outliers : 0.81 % Allowed : 9.96 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.15), residues: 3111 helix: 0.88 (0.16), residues: 1094 sheet: -1.84 (0.29), residues: 325 loop : -1.77 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 998 HIS 0.007 0.001 HIS E 76 PHE 0.020 0.001 PHE D 166 TYR 0.012 0.001 TYR C 87 ARG 0.005 0.000 ARG C 196 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 187 time to evaluate : 4.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7590 (pt) REVERT: B 72 LYS cc_start: 0.8940 (tttp) cc_final: 0.8615 (ttpp) REVERT: B 92 GLU cc_start: 0.7673 (tp30) cc_final: 0.7401 (tp30) REVERT: C 36 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7407 (tm-30) REVERT: C 380 ILE cc_start: 0.8222 (mt) cc_final: 0.7809 (tp) REVERT: C 480 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8022 (tp30) REVERT: D 83 THR cc_start: 0.8854 (t) cc_final: 0.8621 (m) REVERT: D 319 MET cc_start: 0.8368 (mtp) cc_final: 0.8064 (mtp) REVERT: D 661 ARG cc_start: 0.7812 (ptm-80) cc_final: 0.7500 (ptt90) REVERT: D 867 ASN cc_start: 0.8544 (m110) cc_final: 0.8326 (m-40) REVERT: F 284 GLU cc_start: 0.7521 (mp0) cc_final: 0.7110 (mp0) REVERT: F 324 LEU cc_start: 0.7191 (tp) cc_final: 0.6965 (tt) outliers start: 22 outliers final: 17 residues processed: 206 average time/residue: 0.9507 time to fit residues: 301.0931 Evaluate side-chains 201 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 183 time to evaluate : 4.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 1050 TYR Chi-restraints excluded: chain C residue 1150 SER Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 553 GLU Chi-restraints excluded: chain D residue 579 PHE Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 973 TYR Chi-restraints excluded: chain F residue 282 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 189 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 234 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25079 Z= 0.161 Angle : 0.488 6.778 33874 Z= 0.254 Chirality : 0.041 0.142 3870 Planarity : 0.003 0.064 4398 Dihedral : 5.836 141.791 3503 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.62 % Favored : 92.35 % Rotamer: Outliers : 0.52 % Allowed : 10.44 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.16), residues: 3111 helix: 1.08 (0.16), residues: 1091 sheet: -1.71 (0.29), residues: 318 loop : -1.67 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 998 HIS 0.008 0.001 HIS E 76 PHE 0.023 0.001 PHE D 166 TYR 0.011 0.001 TYR C 145 ARG 0.003 0.000 ARG C1064 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 186 time to evaluate : 4.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7440 (pt) REVERT: B 72 LYS cc_start: 0.8931 (tttp) cc_final: 0.8611 (ttpp) REVERT: B 92 GLU cc_start: 0.7653 (tp30) cc_final: 0.7406 (tp30) REVERT: C 36 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7363 (tm-30) REVERT: C 380 ILE cc_start: 0.8224 (mt) cc_final: 0.7824 (tp) REVERT: C 480 GLU cc_start: 0.8272 (tm-30) cc_final: 0.8004 (tp30) REVERT: D 319 MET cc_start: 0.8303 (mtp) cc_final: 0.7984 (mtp) REVERT: D 661 ARG cc_start: 0.7757 (ptm-80) cc_final: 0.7484 (ptt90) REVERT: D 867 ASN cc_start: 0.8556 (m110) cc_final: 0.8318 (m-40) REVERT: F 284 GLU cc_start: 0.7497 (mp0) cc_final: 0.7106 (mp0) outliers start: 14 outliers final: 11 residues processed: 198 average time/residue: 1.0332 time to fit residues: 314.1952 Evaluate side-chains 192 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 180 time to evaluate : 3.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 1050 TYR Chi-restraints excluded: chain C residue 1150 SER Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 907 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 4.9990 chunk 285 optimal weight: 8.9990 chunk 260 optimal weight: 4.9990 chunk 277 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 120 optimal weight: 0.3980 chunk 217 optimal weight: 0.1980 chunk 85 optimal weight: 5.9990 chunk 250 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 276 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25079 Z= 0.196 Angle : 0.494 7.982 33874 Z= 0.257 Chirality : 0.041 0.145 3870 Planarity : 0.004 0.063 4398 Dihedral : 5.815 141.421 3503 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.30 % Favored : 92.67 % Rotamer: Outliers : 0.52 % Allowed : 10.51 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.16), residues: 3111 helix: 1.12 (0.17), residues: 1090 sheet: -1.70 (0.29), residues: 327 loop : -1.66 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 998 HIS 0.007 0.001 HIS E 76 PHE 0.021 0.001 PHE D 166 TYR 0.011 0.001 TYR C 87 ARG 0.002 0.000 ARG C 196 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 4.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7421 (pt) REVERT: B 72 LYS cc_start: 0.8927 (tttp) cc_final: 0.8609 (ttpp) REVERT: B 92 GLU cc_start: 0.7631 (tp30) cc_final: 0.7330 (tp30) REVERT: C 36 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7418 (tm-30) REVERT: C 228 VAL cc_start: 0.6798 (p) cc_final: 0.6588 (p) REVERT: C 380 ILE cc_start: 0.8216 (mt) cc_final: 0.7827 (tp) REVERT: C 480 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7990 (tp30) REVERT: D 319 MET cc_start: 0.8297 (mtp) cc_final: 0.7965 (mtp) REVERT: D 661 ARG cc_start: 0.7834 (ptm-80) cc_final: 0.7531 (ptt90) REVERT: D 867 ASN cc_start: 0.8554 (m110) cc_final: 0.8321 (m-40) REVERT: F 284 GLU cc_start: 0.7493 (mp0) cc_final: 0.7106 (mp0) outliers start: 14 outliers final: 13 residues processed: 196 average time/residue: 0.9888 time to fit residues: 295.6809 Evaluate side-chains 193 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 179 time to evaluate : 4.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 1050 TYR Chi-restraints excluded: chain C residue 1150 SER Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 579 PHE Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 907 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 4.9990 chunk 293 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 204 optimal weight: 0.6980 chunk 307 optimal weight: 20.0000 chunk 283 optimal weight: 8.9990 chunk 245 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25079 Z= 0.253 Angle : 0.513 7.368 33874 Z= 0.268 Chirality : 0.042 0.145 3870 Planarity : 0.004 0.064 4398 Dihedral : 5.886 141.982 3503 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.26 % Favored : 91.71 % Rotamer: Outliers : 0.59 % Allowed : 10.47 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.16), residues: 3111 helix: 1.08 (0.16), residues: 1088 sheet: -1.69 (0.29), residues: 325 loop : -1.70 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 998 HIS 0.008 0.001 HIS E 76 PHE 0.020 0.001 PHE D 166 TYR 0.014 0.001 TYR C 87 ARG 0.002 0.000 ARG C1064 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 182 time to evaluate : 5.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7382 (pt) REVERT: B 72 LYS cc_start: 0.8929 (tttp) cc_final: 0.8612 (ttpp) REVERT: B 92 GLU cc_start: 0.7666 (tp30) cc_final: 0.7360 (tp30) REVERT: C 36 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7381 (tm-30) REVERT: C 228 VAL cc_start: 0.6839 (p) cc_final: 0.6631 (p) REVERT: C 380 ILE cc_start: 0.8187 (mt) cc_final: 0.7835 (tp) REVERT: C 480 GLU cc_start: 0.8310 (tm-30) cc_final: 0.8033 (tp30) REVERT: D 83 THR cc_start: 0.8835 (t) cc_final: 0.8610 (m) REVERT: D 653 ASP cc_start: 0.8430 (t0) cc_final: 0.8096 (m-30) REVERT: D 661 ARG cc_start: 0.7778 (ptm-80) cc_final: 0.7510 (ptt90) REVERT: D 867 ASN cc_start: 0.8578 (m110) cc_final: 0.8336 (m-40) REVERT: F 121 MET cc_start: 0.8464 (mtp) cc_final: 0.8217 (mtm) REVERT: F 284 GLU cc_start: 0.7497 (mp0) cc_final: 0.7092 (mp0) outliers start: 16 outliers final: 14 residues processed: 196 average time/residue: 1.0130 time to fit residues: 304.9056 Evaluate side-chains 196 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 181 time to evaluate : 4.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 1050 TYR Chi-restraints excluded: chain C residue 1150 SER Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 579 PHE Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 907 THR Chi-restraints excluded: chain F residue 282 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 226 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 245 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 252 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.128158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.077043 restraints weight = 110570.977| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.42 r_work: 0.2879 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25079 Z= 0.166 Angle : 0.487 7.161 33874 Z= 0.253 Chirality : 0.041 0.144 3870 Planarity : 0.004 0.062 4398 Dihedral : 5.776 141.333 3503 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.72 % Favored : 93.25 % Rotamer: Outliers : 0.52 % Allowed : 10.58 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.16), residues: 3111 helix: 1.15 (0.16), residues: 1097 sheet: -1.57 (0.29), residues: 323 loop : -1.61 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 998 HIS 0.007 0.001 HIS E 76 PHE 0.020 0.001 PHE D 166 TYR 0.011 0.001 TYR C 145 ARG 0.005 0.000 ARG E 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9168.67 seconds wall clock time: 167 minutes 40.86 seconds (10060.86 seconds total)