Starting phenix.real_space_refine on Thu Feb 22 03:44:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aof_11843/02_2024/7aof_11843_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aof_11843/02_2024/7aof_11843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aof_11843/02_2024/7aof_11843.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aof_11843/02_2024/7aof_11843.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aof_11843/02_2024/7aof_11843_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aof_11843/02_2024/7aof_11843_neut_updated.pdb" } resolution = 2.98 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= 0.000 sd= 0.004 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 4 6.06 5 P 3 5.49 5 Mg 1 5.21 5 S 149 5.16 5 C 21030 2.51 5 N 5424 2.21 5 O 6116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A ARG 687": "NH1" <-> "NH2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 715": "NH1" <-> "NH2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A PHE 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 872": "NH1" <-> "NH2" Residue "A TYR 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 897": "NH1" <-> "NH2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A TYR 913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 914": "OE1" <-> "OE2" Residue "A ARG 1043": "NH1" <-> "NH2" Residue "A PHE 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1211": "NH1" <-> "NH2" Residue "A PHE 1214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1263": "NH1" <-> "NH2" Residue "B ARG 29": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B ARG 250": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B ARG 382": "NH1" <-> "NH2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 478": "NH1" <-> "NH2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B GLU 533": "OE1" <-> "OE2" Residue "B PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B ARG 554": "NH1" <-> "NH2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B ARG 572": "NH1" <-> "NH2" Residue "B ARG 589": "NH1" <-> "NH2" Residue "B ARG 648": "NH1" <-> "NH2" Residue "B ARG 668": "NH1" <-> "NH2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B ARG 792": "NH1" <-> "NH2" Residue "B ARG 794": "NH1" <-> "NH2" Residue "B ARG 808": "NH1" <-> "NH2" Residue "B ARG 821": "NH1" <-> "NH2" Residue "B TYR 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 856": "NH1" <-> "NH2" Residue "B ARG 876": "NH1" <-> "NH2" Residue "B ARG 923": "NH1" <-> "NH2" Residue "B GLU 974": "OE1" <-> "OE2" Residue "B PHE 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 996": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1047": "NH1" <-> "NH2" Residue "B ARG 1058": "NH1" <-> "NH2" Residue "B ARG 1105": "NH1" <-> "NH2" Residue "B PHE 1127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1134": "NH1" <-> "NH2" Residue "C ARG 5": "NH1" <-> "NH2" Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 138": "NH1" <-> "NH2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "F TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 75": "NH1" <-> "NH2" Residue "G ARG 28": "NH1" <-> "NH2" Residue "G PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 210": "NH1" <-> "NH2" Residue "I TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 317": "NH1" <-> "NH2" Residue "I GLU 352": "OE1" <-> "OE2" Residue "I ARG 408": "NH1" <-> "NH2" Residue "I ARG 466": "NH1" <-> "NH2" Residue "I GLU 480": "OE1" <-> "OE2" Residue "I ARG 539": "NH1" <-> "NH2" Residue "I ARG 576": "NH1" <-> "NH2" Residue "I ARG 583": "NH1" <-> "NH2" Residue "I ARG 595": "NH1" <-> "NH2" Residue "I PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 659": "NH1" <-> "NH2" Residue "I TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 710": "NH1" <-> "NH2" Residue "I TYR 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 784": "NH1" <-> "NH2" Residue "J ARG 24": "NH1" <-> "NH2" Residue "S TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 114": "OE1" <-> "OE2" Residue "S ARG 119": "NH1" <-> "NH2" Residue "S TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32727 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 10188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1268, 10188 Classifications: {'peptide': 1268} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 1223} Chain: "B" Number of atoms: 9091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9091 Classifications: {'peptide': 1129} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1076} Chain breaks: 2 Chain: "C" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2484 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 9, 'TRANS': 294} Chain: "E" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1495 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 8, 'TRANS': 175} Chain: "F" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 849 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "G" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1192 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 3, 'TRANS': 149} Chain breaks: 1 Chain: "I" Number of atoms: 5573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5573 Classifications: {'peptide': 665} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 641} Chain breaks: 4 Chain: "J" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 490 Classifications: {'peptide': 61} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 58} Chain: "S" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1360 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 156} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 360 SG CYS A 49 88.711 102.937 62.424 1.00111.55 S ATOM 382 SG CYS A 52 92.441 103.061 61.672 1.00106.51 S ATOM 434 SG CYS A 59 90.886 99.849 63.007 1.00106.93 S ATOM 694 SG CYS A 90 75.616 100.473 109.345 1.00135.81 S ATOM 718 SG CYS A 93 76.868 104.034 109.991 1.00139.72 S ATOM 1016 SG CYS A 130 76.730 101.421 112.791 1.00141.05 S ATOM 1059 SG CYS A 135 73.554 102.962 111.495 1.00143.99 S ATOM 18688 SG CYS B1087 99.143 104.377 76.437 1.00 98.78 S ATOM 18711 SG CYS B1090 95.605 103.182 77.348 1.00101.21 S ATOM 18800 SG CYS B1103 96.072 105.670 74.621 1.00 98.37 S ATOM 18825 SG CYS B1106 96.696 106.749 78.177 1.00102.17 S ATOM 27074 SG CYS I 326 102.516 95.772 38.660 1.00149.52 S ATOM 27387 SG CYS I 363 100.239 92.636 39.608 1.00136.01 S ATOM 27411 SG CYS I 366 103.502 93.325 41.494 1.00142.53 S Time building chain proxies: 17.06, per 1000 atoms: 0.52 Number of scatterers: 32727 At special positions: 0 Unit cell: (163.779, 152.081, 152.081, 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 4 29.99 S 149 16.00 P 3 15.00 Mg 1 11.99 O 6116 8.00 N 5424 7.00 C 21030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS J 7 " - pdb=" SG CYS J 39 " distance=2.04 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: 13.17 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A 62 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 49 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 52 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 59 " pdb=" ZN A1303 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 135 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 90 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 93 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1103 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1090 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1106 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1087 " pdb=" ZN I 801 " pdb="ZN ZN I 801 " - pdb=" NE2 HIS I 328 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 366 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 363 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 326 " Number of angles added : 18 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7726 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 157 helices and 35 sheets defined 37.0% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.02 Creating SS restraints... Processing helix chain 'A' and resid 14 through 18 Processing helix chain 'A' and resid 76 through 88 removed outlier: 3.756A pdb=" N ILE A 79 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N SER A 80 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 162 through 171 removed outlier: 3.545A pdb=" N SER A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 219 through 232 Processing helix chain 'A' and resid 237 through 248 Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 262 through 266 removed outlier: 3.614A pdb=" N ILE A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 322 through 330 Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 406 through 412 removed outlier: 4.769A pdb=" N ASN A 410 " --> pdb=" O GLY A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 Processing helix chain 'A' and resid 441 through 444 Processing helix chain 'A' and resid 459 through 470 removed outlier: 3.615A pdb=" N VAL A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 466 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 487 removed outlier: 6.407A pdb=" N LYS A 485 " --> pdb=" O ASN A 481 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N TYR A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 530 through 533 No H-bonds generated for 'chain 'A' and resid 530 through 533' Processing helix chain 'A' and resid 541 through 548 Processing helix chain 'A' and resid 551 through 572 Processing helix chain 'A' and resid 578 through 581 No H-bonds generated for 'chain 'A' and resid 578 through 581' Processing helix chain 'A' and resid 586 through 614 Processing helix chain 'A' and resid 623 through 655 Processing helix chain 'A' and resid 660 through 666 Processing helix chain 'A' and resid 673 through 680 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 728 through 762 Processing helix chain 'A' and resid 810 through 820 Processing helix chain 'A' and resid 842 through 845 Processing helix chain 'A' and resid 857 through 875 Processing helix chain 'A' and resid 883 through 892 Processing helix chain 'A' and resid 902 through 918 Processing helix chain 'A' and resid 926 through 945 removed outlier: 4.494A pdb=" N SER A 944 " --> pdb=" O GLN A 940 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER A 945 " --> pdb=" O GLN A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 969 Processing helix chain 'A' and resid 985 through 995 Processing helix chain 'A' and resid 1000 through 1003 Processing helix chain 'A' and resid 1024 through 1029 Processing helix chain 'A' and resid 1034 through 1047 removed outlier: 3.519A pdb=" N PHE A1047 " --> pdb=" O ARG A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1092 Proline residue: A1090 - end of helix Processing helix chain 'A' and resid 1132 through 1135 removed outlier: 3.825A pdb=" N SER A1135 " --> pdb=" O GLU A1132 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1132 through 1135' Processing helix chain 'A' and resid 1147 through 1153 Processing helix chain 'A' and resid 1156 through 1170 Processing helix chain 'A' and resid 1176 through 1189 removed outlier: 4.043A pdb=" N GLN A1180 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Proline residue: A1181 - end of helix Processing helix chain 'A' and resid 1208 through 1214 Processing helix chain 'A' and resid 1219 through 1226 Processing helix chain 'A' and resid 1235 through 1240 Processing helix chain 'A' and resid 1248 through 1251 Processing helix chain 'A' and resid 1259 through 1263 Processing helix chain 'B' and resid 9 through 16 Processing helix chain 'B' and resid 29 through 50 removed outlier: 5.270A pdb=" N PHE B 33 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ARG B 45 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU B 46 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 233 through 240 Processing helix chain 'B' and resid 246 through 252 Processing helix chain 'B' and resid 258 through 277 removed outlier: 3.686A pdb=" N LEU B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 297 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 324 through 343 Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 362 through 391 removed outlier: 3.743A pdb=" N PHE B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 415 Processing helix chain 'B' and resid 434 through 439 Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 499 through 515 Processing helix chain 'B' and resid 519 through 521 No H-bonds generated for 'chain 'B' and resid 519 through 521' Processing helix chain 'B' and resid 542 through 557 removed outlier: 5.227A pdb=" N CYS B 546 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG B 557 " --> pdb=" O ARG B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 610 Processing helix chain 'B' and resid 616 through 622 Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 644 through 649 removed outlier: 3.623A pdb=" N MET B 649 " --> pdb=" O GLN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 657 removed outlier: 3.639A pdb=" N LYS B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN B 657 " --> pdb=" O ASP B 653 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 652 through 657' Processing helix chain 'B' and resid 665 through 668 Processing helix chain 'B' and resid 671 through 675 removed outlier: 3.812A pdb=" N SER B 675 " --> pdb=" O TYR B 671 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 671 through 675' Processing helix chain 'B' and resid 679 through 681 No H-bonds generated for 'chain 'B' and resid 679 through 681' Processing helix chain 'B' and resid 684 through 694 Processing helix chain 'B' and resid 726 through 731 Processing helix chain 'B' and resid 762 through 766 Processing helix chain 'B' and resid 796 through 798 No H-bonds generated for 'chain 'B' and resid 796 through 798' Processing helix chain 'B' and resid 899 through 901 No H-bonds generated for 'chain 'B' and resid 899 through 901' Processing helix chain 'B' and resid 918 through 922 Processing helix chain 'B' and resid 926 through 940 removed outlier: 3.515A pdb=" N ILE B 930 " --> pdb=" O ILE B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 976 Processing helix chain 'B' and resid 984 through 989 Processing helix chain 'B' and resid 1055 through 1064 Processing helix chain 'B' and resid 1067 through 1073 Processing helix chain 'B' and resid 1078 through 1080 No H-bonds generated for 'chain 'B' and resid 1078 through 1080' Processing helix chain 'B' and resid 1104 through 1109 Processing helix chain 'B' and resid 1122 through 1133 Processing helix chain 'C' and resid 16 through 29 Processing helix chain 'C' and resid 49 through 58 removed outlier: 3.968A pdb=" N HIS C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 63 No H-bonds generated for 'chain 'C' and resid 61 through 63' Processing helix chain 'C' and resid 66 through 73 removed outlier: 4.049A pdb=" N ILE C 69 " --> pdb=" O TYR C 66 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N HIS C 70 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 73 " --> pdb=" O HIS C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 153 through 157 removed outlier: 3.750A pdb=" N LYS C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 153 through 157' Processing helix chain 'C' and resid 163 through 176 Processing helix chain 'C' and resid 208 through 229 Processing helix chain 'C' and resid 256 through 264 Processing helix chain 'C' and resid 279 through 281 No H-bonds generated for 'chain 'C' and resid 279 through 281' Processing helix chain 'C' and resid 284 through 303 Processing helix chain 'E' and resid 5 through 21 removed outlier: 3.622A pdb=" N LEU E 15 " --> pdb=" O LYS E 11 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 118 through 128 Processing helix chain 'E' and resid 147 through 152 Processing helix chain 'F' and resid 63 through 75 removed outlier: 3.774A pdb=" N ARG F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 95 Processing helix chain 'F' and resid 113 through 122 Processing helix chain 'F' and resid 139 through 141 No H-bonds generated for 'chain 'F' and resid 139 through 141' Processing helix chain 'F' and resid 144 through 160 Processing helix chain 'G' and resid 16 through 18 No H-bonds generated for 'chain 'G' and resid 16 through 18' Processing helix chain 'G' and resid 23 through 35 Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'I' and resid 107 through 118 Processing helix chain 'I' and resid 168 through 185 removed outlier: 4.809A pdb=" N LEU I 172 " --> pdb=" O LYS I 169 " (cutoff:3.500A) Proline residue: I 173 - end of helix removed outlier: 4.845A pdb=" N LEU I 179 " --> pdb=" O GLU I 176 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASP I 180 " --> pdb=" O LYS I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 266 removed outlier: 4.530A pdb=" N LYS I 261 " --> pdb=" O SER I 257 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL I 262 " --> pdb=" O ASP I 258 " (cutoff:3.500A) Proline residue: I 265 - end of helix Processing helix chain 'I' and resid 270 through 278 removed outlier: 5.198A pdb=" N TYR I 275 " --> pdb=" O LEU I 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 290 removed outlier: 4.617A pdb=" N THR I 288 " --> pdb=" O SER I 285 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 335 Processing helix chain 'I' and resid 342 through 352 Processing helix chain 'I' and resid 371 through 373 No H-bonds generated for 'chain 'I' and resid 371 through 373' Processing helix chain 'I' and resid 392 through 396 removed outlier: 3.712A pdb=" N LEU I 396 " --> pdb=" O LYS I 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 392 through 396' Processing helix chain 'I' and resid 398 through 401 No H-bonds generated for 'chain 'I' and resid 398 through 401' Processing helix chain 'I' and resid 405 through 420 removed outlier: 3.922A pdb=" N PHE I 409 " --> pdb=" O HIS I 405 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE I 413 " --> pdb=" O PHE I 409 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 445 removed outlier: 5.071A pdb=" N TYR I 430 " --> pdb=" O VAL I 427 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER I 445 " --> pdb=" O ASP I 442 " (cutoff:3.500A) Processing helix chain 'I' and resid 447 through 453 removed outlier: 4.141A pdb=" N LYS I 452 " --> pdb=" O GLN I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 460 removed outlier: 3.968A pdb=" N LYS I 459 " --> pdb=" O SER I 455 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG I 460 " --> pdb=" O SER I 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 455 through 460' Processing helix chain 'I' and resid 483 through 500 removed outlier: 3.589A pdb=" N LEU I 490 " --> pdb=" O LYS I 486 " (cutoff:3.500A) Processing helix chain 'I' and resid 504 through 513 Processing helix chain 'I' and resid 523 through 537 Processing helix chain 'I' and resid 546 through 558 removed outlier: 3.947A pdb=" N SER I 558 " --> pdb=" O ASP I 554 " (cutoff:3.500A) Processing helix chain 'I' and resid 562 through 580 removed outlier: 3.603A pdb=" N VAL I 579 " --> pdb=" O LEU I 575 " (cutoff:3.500A) Processing helix chain 'I' and resid 639 through 648 Processing helix chain 'I' and resid 688 through 693 removed outlier: 4.133A pdb=" N TYR I 692 " --> pdb=" O LEU I 688 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE I 693 " --> pdb=" O LYS I 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 688 through 693' Processing helix chain 'I' and resid 706 through 709 No H-bonds generated for 'chain 'I' and resid 706 through 709' Processing helix chain 'I' and resid 724 through 741 Processing helix chain 'I' and resid 757 through 770 removed outlier: 3.639A pdb=" N LYS I 770 " --> pdb=" O ILE I 766 " (cutoff:3.500A) Processing helix chain 'I' and resid 774 through 792 removed outlier: 5.778A pdb=" N THR I 783 " --> pdb=" O ASP I 779 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ARG I 784 " --> pdb=" O GLU I 780 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 19 Processing helix chain 'J' and resid 28 through 35 removed outlier: 3.655A pdb=" N SER J 34 " --> pdb=" O ASP J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 46 Processing helix chain 'S' and resid 37 through 50 Processing helix chain 'S' and resid 60 through 62 No H-bonds generated for 'chain 'S' and resid 60 through 62' Processing helix chain 'S' and resid 73 through 80 Processing helix chain 'S' and resid 82 through 84 No H-bonds generated for 'chain 'S' and resid 82 through 84' Processing helix chain 'S' and resid 103 through 109 Processing helix chain 'S' and resid 113 through 130 Processing helix chain 'S' and resid 145 through 147 No H-bonds generated for 'chain 'S' and resid 145 through 147' Processing helix chain 'S' and resid 214 through 216 No H-bonds generated for 'chain 'S' and resid 214 through 216' Processing sheet with id= A, first strand: chain 'A' and resid 6 through 8 Processing sheet with id= B, first strand: chain 'A' and resid 64 through 67 Processing sheet with id= C, first strand: chain 'A' and resid 142 through 144 Processing sheet with id= D, first strand: chain 'A' and resid 285 through 289 Processing sheet with id= E, first strand: chain 'A' and resid 290 through 292 removed outlier: 6.277A pdb=" N ILE A 402 " --> pdb=" O GLY A 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 312 through 316 removed outlier: 7.135A pdb=" N ALA A 369 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL A 334 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 796 through 799 Processing sheet with id= H, first strand: chain 'A' and resid 1121 through 1127 Processing sheet with id= I, first strand: chain 'A' and resid 1008 through 1012 Processing sheet with id= J, first strand: chain 'B' and resid 54 through 59 removed outlier: 6.520A pdb=" N ILE B 66 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N SER B 58 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLU B 64 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYS B 104 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LYS B 116 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL B 106 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE B 114 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 73 through 76 Processing sheet with id= L, first strand: chain 'B' and resid 157 through 159 Processing sheet with id= M, first strand: chain 'B' and resid 221 through 223 removed outlier: 6.618A pdb=" N THR B 189 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL B 182 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N SER B 191 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N PHE B 180 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 443 through 445 Processing sheet with id= O, first strand: chain 'B' and resid 567 through 571 removed outlier: 7.824A pdb=" N ILE B 578 " --> pdb=" O GLY B 527 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ILE B 580 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR B 531 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA B 538 " --> pdb=" O ILE B 530 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE B 532 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LEU B 536 " --> pdb=" O ILE B 532 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 588 through 592 Processing sheet with id= Q, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.816A pdb=" N ILE B 772 " --> pdb=" O ARG B 875 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 892 through 897 removed outlier: 7.528A pdb=" N ILE B 760 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL B 896 " --> pdb=" O ILE B 760 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE B1009 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 858 through 861 Processing sheet with id= T, first strand: chain 'C' and resid 5 through 13 removed outlier: 3.582A pdb=" N ILE C 188 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 37 through 43 removed outlier: 3.829A pdb=" N ILE C 37 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU C 140 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASN C 43 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR C 138 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 251 through 253 Processing sheet with id= W, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= X, first strand: chain 'E' and resid 63 through 65 removed outlier: 6.224A pdb=" N ILE E 82 " --> pdb=" O PHE E 64 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 113 through 115 Processing sheet with id= Z, first strand: chain 'F' and resid 129 through 131 Processing sheet with id= AA, first strand: chain 'G' and resid 3 through 15 removed outlier: 3.524A pdb=" N LYS G 47 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA G 77 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ALA G 45 " --> pdb=" O ALA G 77 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 136 through 140 removed outlier: 4.291A pdb=" N VAL G 97 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE G 152 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LYS G 107 " --> pdb=" O PHE G 152 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE G 154 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASN G 157 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU G 141 " --> pdb=" O ASN G 157 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 124 through 126 Processing sheet with id= AD, first strand: chain 'I' and resid 121 through 123 Processing sheet with id= AE, first strand: chain 'I' and resid 161 through 166 removed outlier: 6.592A pdb=" N ILE I 128 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE I 164 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE I 130 " --> pdb=" O ILE I 164 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE I 166 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL I 132 " --> pdb=" O PHE I 166 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'I' and resid 209 through 217 Processing sheet with id= AG, first strand: chain 'I' and resid 354 through 357 Processing sheet with id= AH, first strand: chain 'I' and resid 697 through 701 removed outlier: 4.326A pdb=" N ILE I 658 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'I' and resid 668 through 670 1129 hydrogen bonds defined for protein. 2991 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: 11.87 Time building geometry restraints manager: 14.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10437 1.34 - 1.46: 7462 1.46 - 1.58: 15244 1.58 - 1.70: 12 1.70 - 1.82: 236 Bond restraints: 33391 Sorted by residual: bond pdb=" C LEU E 13 " pdb=" N CYS E 14 " ideal model delta sigma weight residual 1.332 1.304 0.027 1.35e-02 5.49e+03 4.15e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" N GLN A 459 " pdb=" CA GLN A 459 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.29e-02 6.01e+03 2.15e+00 bond pdb=" C ILE C 177 " pdb=" N ASP C 178 " ideal model delta sigma weight residual 1.339 1.414 -0.074 5.57e-02 3.22e+02 1.78e+00 bond pdb=" N ASN B 320 " pdb=" CA ASN B 320 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.40e-01 ... (remaining 33386 not shown) Histogram of bond angle deviations from ideal: 100.53 - 107.22: 924 107.22 - 113.92: 19003 113.92 - 120.61: 13397 120.61 - 127.31: 11559 127.31 - 134.00: 263 Bond angle restraints: 45146 Sorted by residual: angle pdb=" CG1 VAL E 170 " pdb=" CB VAL E 170 " pdb=" CG2 VAL E 170 " ideal model delta sigma weight residual 110.80 122.00 -11.20 2.20e+00 2.07e-01 2.59e+01 angle pdb=" CG1 VAL C 111 " pdb=" CB VAL C 111 " pdb=" CG2 VAL C 111 " ideal model delta sigma weight residual 110.80 121.62 -10.82 2.20e+00 2.07e-01 2.42e+01 angle pdb=" CA VAL C 111 " pdb=" CB VAL C 111 " pdb=" CG1 VAL C 111 " ideal model delta sigma weight residual 110.40 116.90 -6.50 1.70e+00 3.46e-01 1.46e+01 angle pdb=" CA VAL E 170 " pdb=" CB VAL E 170 " pdb=" CG1 VAL E 170 " ideal model delta sigma weight residual 110.40 116.84 -6.44 1.70e+00 3.46e-01 1.44e+01 angle pdb=" CA VAL E 170 " pdb=" CB VAL E 170 " pdb=" CG2 VAL E 170 " ideal model delta sigma weight residual 110.40 116.81 -6.41 1.70e+00 3.46e-01 1.42e+01 ... (remaining 45141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 19510 17.86 - 35.73: 630 35.73 - 53.59: 119 53.59 - 71.45: 34 71.45 - 89.31: 10 Dihedral angle restraints: 20303 sinusoidal: 8351 harmonic: 11952 Sorted by residual: dihedral pdb=" CB CYS J 7 " pdb=" SG CYS J 7 " pdb=" SG CYS J 39 " pdb=" CB CYS J 39 " ideal model delta sinusoidal sigma weight residual -86.00 -139.67 53.67 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" CA ILE A 458 " pdb=" C ILE A 458 " pdb=" N GLN A 459 " pdb=" CA GLN A 459 " ideal model delta harmonic sigma weight residual -180.00 -154.08 -25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ASN C 245 " pdb=" C ASN C 245 " pdb=" N PRO C 246 " pdb=" CA PRO C 246 " ideal model delta harmonic sigma weight residual 180.00 157.17 22.83 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 20300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.297: 5112 0.297 - 0.594: 0 0.594 - 0.892: 0 0.892 - 1.189: 0 1.189 - 1.486: 2 Chirality restraints: 5114 Sorted by residual: chirality pdb=" CB VAL E 170 " pdb=" CA VAL E 170 " pdb=" CG1 VAL E 170 " pdb=" CG2 VAL E 170 " both_signs ideal model delta sigma weight residual False -2.63 -1.14 -1.49 2.00e-01 2.50e+01 5.52e+01 chirality pdb=" CB VAL C 111 " pdb=" CA VAL C 111 " pdb=" CG1 VAL C 111 " pdb=" CG2 VAL C 111 " both_signs ideal model delta sigma weight residual False -2.63 -1.20 -1.43 2.00e-01 2.50e+01 5.10e+01 chirality pdb=" CA ILE C 59 " pdb=" N ILE C 59 " pdb=" C ILE C 59 " pdb=" CB ILE C 59 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 5111 not shown) Planarity restraints: 5712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 41 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.74e+00 pdb=" C PHE B 41 " 0.029 2.00e-02 2.50e+03 pdb=" O PHE B 41 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE B 42 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 938 " 0.013 2.00e-02 2.50e+03 1.15e-02 2.32e+00 pdb=" CG PHE A 938 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 938 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 938 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 938 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 938 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 938 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 459 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" C GLN A 459 " -0.025 2.00e-02 2.50e+03 pdb=" O GLN A 459 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP A 460 " 0.008 2.00e-02 2.50e+03 ... (remaining 5709 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 331 2.57 - 3.15: 28827 3.15 - 3.73: 49984 3.73 - 4.32: 73716 4.32 - 4.90: 122358 Nonbonded interactions: 275216 Sorted by model distance: nonbonded pdb=" N CYS I 366 " pdb="ZN ZN I 801 " model vdw 1.984 2.310 nonbonded pdb=" OD1 ASP A 415 " pdb="MG MG A1301 " model vdw 2.009 2.170 nonbonded pdb=" OD1 ASP A 419 " pdb="MG MG A1301 " model vdw 2.015 2.170 nonbonded pdb=" OE2 GLU I 250 " pdb=" OG SER I 280 " model vdw 2.081 2.440 nonbonded pdb=" O THR B 887 " pdb=" OG SER B 888 " model vdw 2.135 2.440 ... (remaining 275211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.630 Check model and map are aligned: 0.420 Set scattering table: 0.270 Process input model: 90.150 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.120 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:14.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 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 : 0.002 0.074 33391 Z= 0.153 Angle : 0.458 11.202 45146 Z= 0.264 Chirality : 0.050 1.486 5114 Planarity : 0.002 0.033 5712 Dihedral : 9.854 89.314 12574 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.91 % Favored : 95.04 % Rotamer: Outliers : 1.81 % Allowed : 4.16 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % 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: 0.39 (0.14), residues: 3991 helix: 1.49 (0.14), residues: 1493 sheet: -0.09 (0.23), residues: 534 loop : -0.56 (0.15), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 365 HIS 0.003 0.001 HIS B 318 PHE 0.026 0.001 PHE A 938 TYR 0.017 0.001 TYR B 377 ARG 0.003 0.000 ARG S 250 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 379 time to evaluate : 4.086 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 146 LYS cc_start: 0.9210 (ttmt) cc_final: 0.9000 (ttpm) REVERT: A 238 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8334 (mm-40) REVERT: A 1031 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8317 (mm-30) REVERT: B 67 MET cc_start: 0.8226 (mmm) cc_final: 0.7791 (mmm) REVERT: B 159 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8145 (p0) REVERT: B 256 MET cc_start: 0.8975 (mmt) cc_final: 0.8678 (mmt) REVERT: B 506 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7534 (tm-30) REVERT: B 719 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8471 (pt0) REVERT: E 18 GLU cc_start: 0.9080 (tp30) cc_final: 0.8640 (tp30) REVERT: E 69 ILE cc_start: 0.9012 (mt) cc_final: 0.8650 (mp) REVERT: E 86 SER cc_start: 0.9536 (m) cc_final: 0.9144 (p) REVERT: G 100 GLN cc_start: 0.8822 (mt0) cc_final: 0.8517 (mp10) REVERT: G 103 ASP cc_start: 0.8719 (p0) cc_final: 0.8381 (p0) REVERT: G 124 PHE cc_start: 0.7903 (m-80) cc_final: 0.7628 (m-80) REVERT: G 131 TYR cc_start: 0.7247 (m-80) cc_final: 0.6882 (m-80) REVERT: I 121 MET cc_start: 0.8477 (mmt) cc_final: 0.7984 (mmt) REVERT: I 195 CYS cc_start: 0.9005 (m) cc_final: 0.8618 (m) REVERT: I 281 TYR cc_start: 0.8519 (t80) cc_final: 0.8235 (t80) REVERT: I 444 ASN cc_start: 0.9005 (t0) cc_final: 0.8404 (p0) REVERT: J 51 GLN cc_start: 0.8052 (tp-100) cc_final: 0.7705 (tp40) REVERT: J 61 ASP cc_start: 0.8268 (t70) cc_final: 0.7908 (t70) REVERT: S 37 LEU cc_start: 0.8072 (mt) cc_final: 0.7797 (tp) outliers start: 67 outliers final: 18 residues processed: 436 average time/residue: 1.4617 time to fit residues: 753.4442 Evaluate side-chains 248 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 227 time to evaluate : 3.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 638 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain S residue 103 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 336 optimal weight: 0.5980 chunk 302 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 203 optimal weight: 0.7980 chunk 161 optimal weight: 0.7980 chunk 312 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 362 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN B 389 HIS I 197 HIS I 567 HIS J 51 GLN S 97 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 33391 Z= 0.189 Angle : 0.528 7.935 45146 Z= 0.275 Chirality : 0.043 0.231 5114 Planarity : 0.004 0.046 5712 Dihedral : 5.442 85.261 4450 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.89 % Favored : 95.09 % Rotamer: Outliers : 1.94 % Allowed : 9.37 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % 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: 0.47 (0.14), residues: 3991 helix: 1.50 (0.14), residues: 1495 sheet: 0.01 (0.23), residues: 532 loop : -0.49 (0.15), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 365 HIS 0.010 0.001 HIS B 389 PHE 0.028 0.001 PHE A 938 TYR 0.019 0.001 TYR S 134 ARG 0.007 0.000 ARG C 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 248 time to evaluate : 3.877 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 226 MET cc_start: 0.8672 (mmm) cc_final: 0.8407 (mmm) REVERT: A 961 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8604 (t80) REVERT: A 1031 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8328 (mm-30) REVERT: B 67 MET cc_start: 0.8267 (mmm) cc_final: 0.7958 (mmm) REVERT: B 159 ASN cc_start: 0.8998 (OUTLIER) cc_final: 0.8081 (p0) REVERT: B 506 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7733 (tm-30) REVERT: B 1056 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8427 (mtp) REVERT: E 18 GLU cc_start: 0.9087 (tp30) cc_final: 0.8404 (tp30) REVERT: E 86 SER cc_start: 0.9446 (m) cc_final: 0.9184 (p) REVERT: G 100 GLN cc_start: 0.8793 (mt0) cc_final: 0.8503 (mp10) REVERT: G 103 ASP cc_start: 0.8799 (p0) cc_final: 0.8351 (p0) REVERT: G 107 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8636 (mtmt) REVERT: G 124 PHE cc_start: 0.7919 (m-80) cc_final: 0.7623 (m-80) REVERT: G 131 TYR cc_start: 0.7232 (m-80) cc_final: 0.6771 (m-80) REVERT: G 145 GLN cc_start: 0.8579 (mt0) cc_final: 0.8354 (mt0) REVERT: I 168 MET cc_start: 0.9320 (OUTLIER) cc_final: 0.8987 (mtp) REVERT: I 205 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8462 (ptpp) REVERT: I 281 TYR cc_start: 0.8511 (t80) cc_final: 0.8221 (t80) REVERT: I 444 ASN cc_start: 0.8908 (t0) cc_final: 0.8385 (p0) REVERT: I 569 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8520 (tp40) REVERT: I 573 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8876 (mm) REVERT: I 643 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.9122 (tptp) REVERT: J 51 GLN cc_start: 0.8336 (tp40) cc_final: 0.7937 (tp40) REVERT: J 61 ASP cc_start: 0.8226 (t70) cc_final: 0.7856 (t70) outliers start: 72 outliers final: 24 residues processed: 301 average time/residue: 1.4326 time to fit residues: 515.6639 Evaluate side-chains 247 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 214 time to evaluate : 3.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 1056 MET Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain I residue 168 MET Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 547 ASP Chi-restraints excluded: chain I residue 558 SER Chi-restraints excluded: chain I residue 569 GLN Chi-restraints excluded: chain I residue 573 LEU Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 105 ASP Chi-restraints excluded: chain S residue 151 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 201 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 301 optimal weight: 0.7980 chunk 246 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 362 optimal weight: 3.9990 chunk 392 optimal weight: 5.9990 chunk 323 optimal weight: 7.9990 chunk 359 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 291 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 HIS I 197 HIS I 567 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 33391 Z= 0.339 Angle : 0.558 9.014 45146 Z= 0.290 Chirality : 0.044 0.205 5114 Planarity : 0.004 0.042 5712 Dihedral : 5.325 83.090 4434 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.46 % Favored : 94.51 % Rotamer: Outliers : 2.56 % Allowed : 9.96 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % 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: 0.37 (0.14), residues: 3991 helix: 1.37 (0.14), residues: 1511 sheet: -0.01 (0.23), residues: 517 loop : -0.53 (0.15), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1054 HIS 0.015 0.001 HIS I 197 PHE 0.031 0.001 PHE A 938 TYR 0.019 0.001 TYR S 134 ARG 0.010 0.001 ARG C 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 228 time to evaluate : 3.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.7803 (pm20) cc_final: 0.7491 (pm20) REVERT: A 226 MET cc_start: 0.8757 (mmm) cc_final: 0.8417 (mmm) REVERT: A 631 GLU cc_start: 0.8219 (pp20) cc_final: 0.7966 (pp20) REVERT: A 1031 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8357 (mm-30) REVERT: B 64 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8709 (pp20) REVERT: B 67 MET cc_start: 0.8281 (mmm) cc_final: 0.7911 (mmm) REVERT: B 159 ASN cc_start: 0.8992 (OUTLIER) cc_final: 0.8246 (p0) REVERT: B 506 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7983 (tm-30) REVERT: B 719 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8428 (pt0) REVERT: B 819 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8360 (mtt) REVERT: B 1056 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8459 (mtp) REVERT: E 55 ASP cc_start: 0.7786 (t70) cc_final: 0.6051 (t0) REVERT: E 86 SER cc_start: 0.9467 (m) cc_final: 0.9200 (p) REVERT: E 120 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8506 (mp0) REVERT: E 174 GLU cc_start: 0.8389 (tp30) cc_final: 0.8184 (mm-30) REVERT: G 100 GLN cc_start: 0.8860 (mt0) cc_final: 0.8527 (mp10) REVERT: G 103 ASP cc_start: 0.8856 (p0) cc_final: 0.8374 (p0) REVERT: G 107 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8710 (mtmt) REVERT: G 124 PHE cc_start: 0.7918 (m-80) cc_final: 0.7605 (m-80) REVERT: G 131 TYR cc_start: 0.6893 (m-80) cc_final: 0.6609 (m-80) REVERT: I 121 MET cc_start: 0.8490 (mmt) cc_final: 0.7910 (mmt) REVERT: I 205 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8560 (ptpp) REVERT: I 281 TYR cc_start: 0.8545 (t80) cc_final: 0.8273 (t80) REVERT: I 444 ASN cc_start: 0.8943 (t0) cc_final: 0.8424 (p0) REVERT: I 643 LYS cc_start: 0.9378 (OUTLIER) cc_final: 0.9109 (tptp) REVERT: J 51 GLN cc_start: 0.8355 (tp40) cc_final: 0.7958 (tp40) REVERT: S 141 ASP cc_start: 0.8032 (t0) cc_final: 0.7801 (t0) outliers start: 95 outliers final: 39 residues processed: 294 average time/residue: 1.4331 time to fit residues: 503.6883 Evaluate side-chains 260 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 212 time to evaluate : 3.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 819 MET Chi-restraints excluded: chain B residue 1056 MET Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain I residue 168 MET Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 547 ASP Chi-restraints excluded: chain I residue 558 SER Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 638 THR Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 105 ASP Chi-restraints excluded: chain S residue 146 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 358 optimal weight: 2.9990 chunk 272 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 243 optimal weight: 0.9980 chunk 364 optimal weight: 9.9990 chunk 385 optimal weight: 10.0000 chunk 190 optimal weight: 0.8980 chunk 345 optimal weight: 0.0670 chunk 103 optimal weight: 0.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN B 779 GLN ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 567 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 33391 Z= 0.155 Angle : 0.503 10.656 45146 Z= 0.261 Chirality : 0.042 0.155 5114 Planarity : 0.003 0.049 5712 Dihedral : 5.202 83.605 4434 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.94 % Favored : 95.04 % Rotamer: Outliers : 2.00 % Allowed : 10.48 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % 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: 0.45 (0.14), residues: 3991 helix: 1.44 (0.14), residues: 1500 sheet: 0.06 (0.23), residues: 511 loop : -0.48 (0.15), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1054 HIS 0.009 0.001 HIS I 197 PHE 0.028 0.001 PHE A 938 TYR 0.019 0.001 TYR I 492 ARG 0.010 0.000 ARG C 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 234 time to evaluate : 3.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8464 (m) REVERT: A 226 MET cc_start: 0.8720 (mmm) cc_final: 0.8498 (mmm) REVERT: A 261 ASN cc_start: 0.9070 (OUTLIER) cc_final: 0.8838 (p0) REVERT: A 631 GLU cc_start: 0.8256 (pp20) cc_final: 0.7914 (pp20) REVERT: A 961 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8517 (t80) REVERT: A 1031 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8356 (mm-30) REVERT: B 67 MET cc_start: 0.8215 (mmm) cc_final: 0.7798 (mmm) REVERT: B 159 ASN cc_start: 0.9037 (OUTLIER) cc_final: 0.8310 (p0) REVERT: B 719 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8410 (pt0) REVERT: B 819 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8357 (mtt) REVERT: E 57 MET cc_start: 0.8218 (mmm) cc_final: 0.7920 (mmm) REVERT: E 67 SER cc_start: 0.9180 (p) cc_final: 0.8949 (p) REVERT: E 86 SER cc_start: 0.9440 (m) cc_final: 0.9183 (p) REVERT: G 86 ARG cc_start: 0.8040 (mtp180) cc_final: 0.7701 (tpt-90) REVERT: G 100 GLN cc_start: 0.8838 (mt0) cc_final: 0.8519 (mp10) REVERT: G 107 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8680 (mtmt) REVERT: G 124 PHE cc_start: 0.7926 (m-80) cc_final: 0.7653 (m-80) REVERT: G 131 TYR cc_start: 0.6931 (m-80) cc_final: 0.6331 (m-80) REVERT: I 121 MET cc_start: 0.8531 (mmt) cc_final: 0.8173 (mmt) REVERT: I 168 MET cc_start: 0.9353 (OUTLIER) cc_final: 0.9050 (mtp) REVERT: I 205 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8563 (ptpp) REVERT: I 281 TYR cc_start: 0.8523 (t80) cc_final: 0.8261 (t80) REVERT: I 444 ASN cc_start: 0.8883 (t0) cc_final: 0.8421 (p0) REVERT: I 643 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.9100 (tptp) REVERT: J 51 GLN cc_start: 0.8360 (tp40) cc_final: 0.7962 (tp40) REVERT: S 104 CYS cc_start: 0.9216 (m) cc_final: 0.8471 (p) REVERT: S 141 ASP cc_start: 0.8010 (t0) cc_final: 0.7725 (t0) outliers start: 74 outliers final: 27 residues processed: 286 average time/residue: 1.4553 time to fit residues: 497.5900 Evaluate side-chains 245 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 208 time to evaluate : 3.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 819 MET Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain I residue 168 MET Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 518 VAL Chi-restraints excluded: chain I residue 638 THR Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 105 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 321 optimal weight: 6.9990 chunk 218 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 287 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 329 optimal weight: 0.8980 chunk 266 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 chunk 346 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 ASN I 197 HIS I 567 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 33391 Z= 0.455 Angle : 0.609 10.762 45146 Z= 0.315 Chirality : 0.045 0.200 5114 Planarity : 0.004 0.045 5712 Dihedral : 5.453 82.587 4433 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.01 % Favored : 93.96 % Rotamer: Outliers : 2.54 % Allowed : 11.37 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % 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: 0.24 (0.14), residues: 3991 helix: 1.24 (0.14), residues: 1516 sheet: -0.09 (0.23), residues: 517 loop : -0.59 (0.15), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1054 HIS 0.007 0.001 HIS I 405 PHE 0.031 0.002 PHE A 938 TYR 0.024 0.002 TYR B 377 ARG 0.007 0.001 ARG G 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 202 time to evaluate : 4.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASN cc_start: 0.9162 (OUTLIER) cc_final: 0.8819 (p0) REVERT: A 631 GLU cc_start: 0.8300 (pp20) cc_final: 0.7962 (pp20) REVERT: A 1031 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8375 (mm-30) REVERT: B 64 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8670 (pp20) REVERT: B 67 MET cc_start: 0.8345 (mmm) cc_final: 0.7879 (mmm) REVERT: B 159 ASN cc_start: 0.9022 (OUTLIER) cc_final: 0.8373 (p0) REVERT: E 86 SER cc_start: 0.9458 (m) cc_final: 0.9195 (p) REVERT: E 120 GLU cc_start: 0.8751 (mp0) cc_final: 0.8547 (mp0) REVERT: E 144 GLU cc_start: 0.8420 (pt0) cc_final: 0.7707 (pm20) REVERT: F 110 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.9153 (mtpt) REVERT: G 86 ARG cc_start: 0.7865 (mtp180) cc_final: 0.7533 (tpt-90) REVERT: G 100 GLN cc_start: 0.8889 (mt0) cc_final: 0.8524 (mp10) REVERT: G 107 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8730 (mtmt) REVERT: G 124 PHE cc_start: 0.7927 (m-80) cc_final: 0.7649 (m-80) REVERT: G 131 TYR cc_start: 0.6947 (m-80) cc_final: 0.6516 (m-80) REVERT: I 205 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8632 (ptpp) REVERT: I 281 TYR cc_start: 0.8561 (t80) cc_final: 0.8301 (t80) REVERT: I 643 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.9106 (tptp) REVERT: J 51 GLN cc_start: 0.8410 (tp40) cc_final: 0.7944 (tp40) REVERT: S 141 ASP cc_start: 0.8149 (t0) cc_final: 0.7873 (t0) outliers start: 94 outliers final: 52 residues processed: 272 average time/residue: 1.4068 time to fit residues: 459.8425 Evaluate side-chains 255 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 196 time to evaluate : 4.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 92 HIS Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 168 MET Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 379 ASP Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 547 ASP Chi-restraints excluded: chain I residue 558 SER Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 638 THR Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain I residue 788 LEU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 105 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 129 optimal weight: 0.7980 chunk 347 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 386 optimal weight: 0.8980 chunk 320 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 202 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 567 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.089 33391 Z= 0.157 Angle : 0.519 12.224 45146 Z= 0.268 Chirality : 0.042 0.163 5114 Planarity : 0.003 0.064 5712 Dihedral : 5.283 83.933 4433 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.06 % Favored : 94.91 % Rotamer: Outliers : 2.02 % Allowed : 11.93 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % 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: 0.35 (0.14), residues: 3991 helix: 1.33 (0.14), residues: 1507 sheet: 0.02 (0.23), residues: 513 loop : -0.54 (0.15), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1054 HIS 0.028 0.001 HIS I 197 PHE 0.028 0.001 PHE A 938 TYR 0.024 0.001 TYR A 264 ARG 0.015 0.000 ARG C 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 220 time to evaluate : 4.050 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 149 VAL cc_start: 0.8724 (OUTLIER) cc_final: 0.8502 (m) REVERT: A 261 ASN cc_start: 0.9196 (OUTLIER) cc_final: 0.8932 (p0) REVERT: A 631 GLU cc_start: 0.8276 (pp20) cc_final: 0.7892 (pp20) REVERT: A 1031 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8361 (mm-30) REVERT: B 64 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8677 (pp20) REVERT: B 67 MET cc_start: 0.8243 (mmm) cc_final: 0.7764 (mmm) REVERT: B 159 ASN cc_start: 0.9030 (OUTLIER) cc_final: 0.8387 (p0) REVERT: B 575 MET cc_start: 0.9276 (mpp) cc_final: 0.9016 (mpt) REVERT: E 67 SER cc_start: 0.9200 (p) cc_final: 0.8987 (p) REVERT: E 86 SER cc_start: 0.9457 (m) cc_final: 0.9203 (p) REVERT: E 120 GLU cc_start: 0.8696 (mp0) cc_final: 0.8460 (mp0) REVERT: E 144 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7855 (pm20) REVERT: G 100 GLN cc_start: 0.8864 (mt0) cc_final: 0.8503 (mp10) REVERT: G 107 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8658 (mtmt) REVERT: G 124 PHE cc_start: 0.7929 (m-80) cc_final: 0.7679 (m-80) REVERT: G 131 TYR cc_start: 0.6976 (m-80) cc_final: 0.6411 (m-80) REVERT: I 121 MET cc_start: 0.8534 (mmt) cc_final: 0.8111 (mmt) REVERT: I 205 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8594 (ptpp) REVERT: I 281 TYR cc_start: 0.8533 (t80) cc_final: 0.8264 (t80) REVERT: I 643 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9096 (tptp) REVERT: J 51 GLN cc_start: 0.8400 (tp40) cc_final: 0.7986 (tp40) REVERT: S 104 CYS cc_start: 0.9189 (m) cc_final: 0.8458 (p) REVERT: S 141 ASP cc_start: 0.8134 (t0) cc_final: 0.7845 (t0) outliers start: 75 outliers final: 35 residues processed: 280 average time/residue: 1.4657 time to fit residues: 490.9171 Evaluate side-chains 250 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 207 time to evaluate : 3.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 558 SER Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 638 THR Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 105 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 372 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 219 optimal weight: 5.9990 chunk 281 optimal weight: 8.9990 chunk 218 optimal weight: 0.1980 chunk 324 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 384 optimal weight: 2.9990 chunk 240 optimal weight: 4.9990 chunk 234 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** E 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 HIS ** I 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 567 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 33391 Z= 0.209 Angle : 0.526 11.063 45146 Z= 0.269 Chirality : 0.042 0.164 5114 Planarity : 0.003 0.038 5712 Dihedral : 5.202 83.299 4433 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.02 % Allowed : 12.34 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % 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: 0.36 (0.14), residues: 3991 helix: 1.36 (0.14), residues: 1501 sheet: 0.04 (0.23), residues: 514 loop : -0.54 (0.15), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1054 HIS 0.006 0.001 HIS B 409 PHE 0.029 0.001 PHE A 938 TYR 0.022 0.001 TYR B 377 ARG 0.007 0.000 ARG G 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 214 time to evaluate : 3.834 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 149 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8501 (m) REVERT: A 261 ASN cc_start: 0.9204 (OUTLIER) cc_final: 0.8994 (p0) REVERT: A 631 GLU cc_start: 0.8297 (pp20) cc_final: 0.7893 (pp20) REVERT: A 1031 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8373 (mm-30) REVERT: B 64 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8670 (pp20) REVERT: B 67 MET cc_start: 0.8260 (mmm) cc_final: 0.7757 (mmm) REVERT: B 159 ASN cc_start: 0.9034 (OUTLIER) cc_final: 0.8433 (p0) REVERT: B 575 MET cc_start: 0.9278 (mpp) cc_final: 0.9021 (mpt) REVERT: E 67 SER cc_start: 0.9191 (p) cc_final: 0.8973 (p) REVERT: E 86 SER cc_start: 0.9459 (m) cc_final: 0.9211 (p) REVERT: E 120 GLU cc_start: 0.8688 (mp0) cc_final: 0.8456 (mp0) REVERT: E 144 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7894 (pm20) REVERT: G 86 ARG cc_start: 0.7908 (mtp180) cc_final: 0.7390 (tpt-90) REVERT: G 100 GLN cc_start: 0.8878 (mt0) cc_final: 0.8508 (mp10) REVERT: G 107 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8693 (mtmt) REVERT: G 124 PHE cc_start: 0.7928 (m-80) cc_final: 0.7682 (m-80) REVERT: G 131 TYR cc_start: 0.6784 (m-80) cc_final: 0.6385 (m-80) REVERT: I 121 MET cc_start: 0.8532 (mmt) cc_final: 0.8113 (mmt) REVERT: I 168 MET cc_start: 0.9370 (OUTLIER) cc_final: 0.9076 (mtp) REVERT: I 205 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8610 (ptpp) REVERT: I 281 TYR cc_start: 0.8541 (t80) cc_final: 0.8273 (t80) REVERT: I 643 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.9106 (tptp) REVERT: J 51 GLN cc_start: 0.8428 (tp40) cc_final: 0.8005 (tp40) REVERT: S 104 CYS cc_start: 0.9181 (m) cc_final: 0.8457 (p) REVERT: S 141 ASP cc_start: 0.8119 (t0) cc_final: 0.7816 (t0) outliers start: 75 outliers final: 44 residues processed: 274 average time/residue: 1.4197 time to fit residues: 466.7768 Evaluate side-chains 257 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 204 time to evaluate : 3.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 92 HIS Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 168 MET Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 547 ASP Chi-restraints excluded: chain I residue 558 SER Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 638 THR Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 105 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 237 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 229 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 302 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 HIS ** I 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 444 ASN I 567 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 33391 Z= 0.299 Angle : 0.563 13.915 45146 Z= 0.287 Chirality : 0.043 0.166 5114 Planarity : 0.003 0.038 5712 Dihedral : 5.247 82.998 4430 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.00 % Allowed : 12.47 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % 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: 0.31 (0.14), residues: 3991 helix: 1.33 (0.14), residues: 1500 sheet: -0.00 (0.23), residues: 512 loop : -0.58 (0.15), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1054 HIS 0.010 0.001 HIS I 197 PHE 0.030 0.001 PHE A 938 TYR 0.029 0.001 TYR A 264 ARG 0.012 0.000 ARG C 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 216 time to evaluate : 4.079 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 261 ASN cc_start: 0.9210 (OUTLIER) cc_final: 0.8975 (p0) REVERT: A 631 GLU cc_start: 0.8301 (pp20) cc_final: 0.7898 (pp20) REVERT: A 1031 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8381 (mm-30) REVERT: B 64 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8635 (pp20) REVERT: B 67 MET cc_start: 0.8300 (mmm) cc_final: 0.7767 (mmm) REVERT: B 159 ASN cc_start: 0.9035 (OUTLIER) cc_final: 0.8478 (p0) REVERT: B 575 MET cc_start: 0.9272 (mpp) cc_final: 0.8988 (mpt) REVERT: C 250 MET cc_start: 0.9089 (mmm) cc_final: 0.8545 (tpp) REVERT: E 67 SER cc_start: 0.9248 (p) cc_final: 0.9040 (p) REVERT: E 86 SER cc_start: 0.9460 (m) cc_final: 0.9200 (p) REVERT: E 144 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7910 (pm20) REVERT: G 86 ARG cc_start: 0.7894 (mtp180) cc_final: 0.7398 (tpt-90) REVERT: G 100 GLN cc_start: 0.8893 (mt0) cc_final: 0.8507 (mp10) REVERT: G 107 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8721 (mtmt) REVERT: G 110 ARG cc_start: 0.7371 (mmm160) cc_final: 0.6979 (tpm-80) REVERT: G 124 PHE cc_start: 0.7943 (m-80) cc_final: 0.7696 (m-80) REVERT: G 131 TYR cc_start: 0.6822 (m-80) cc_final: 0.6401 (m-80) REVERT: I 205 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8589 (ptpp) REVERT: I 281 TYR cc_start: 0.8548 (t80) cc_final: 0.8274 (t80) REVERT: I 486 LYS cc_start: 0.8614 (mttt) cc_final: 0.8275 (ptpp) REVERT: I 643 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.9114 (tptp) REVERT: J 51 GLN cc_start: 0.8447 (tp40) cc_final: 0.8007 (tp40) REVERT: S 104 CYS cc_start: 0.9202 (m) cc_final: 0.8511 (p) REVERT: S 141 ASP cc_start: 0.8239 (t0) cc_final: 0.7963 (t0) outliers start: 74 outliers final: 49 residues processed: 275 average time/residue: 1.4579 time to fit residues: 483.4409 Evaluate side-chains 264 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 208 time to evaluate : 3.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 92 HIS Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 547 ASP Chi-restraints excluded: chain I residue 558 SER Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 638 THR Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain I residue 666 THR Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 105 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 349 optimal weight: 2.9990 chunk 368 optimal weight: 6.9990 chunk 336 optimal weight: 2.9990 chunk 358 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 281 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 323 optimal weight: 5.9990 chunk 338 optimal weight: 7.9990 chunk 357 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 HIS ** I 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 444 ASN I 567 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 33391 Z= 0.301 Angle : 0.573 11.868 45146 Z= 0.293 Chirality : 0.043 0.166 5114 Planarity : 0.004 0.079 5712 Dihedral : 5.288 82.979 4430 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.86 % Allowed : 12.80 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % 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: 0.26 (0.14), residues: 3991 helix: 1.27 (0.14), residues: 1507 sheet: -0.06 (0.23), residues: 519 loop : -0.59 (0.15), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1054 HIS 0.017 0.001 HIS I 197 PHE 0.030 0.001 PHE A 938 TYR 0.023 0.001 TYR B 377 ARG 0.019 0.000 ARG C 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 211 time to evaluate : 3.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASN cc_start: 0.9179 (OUTLIER) cc_final: 0.8962 (p0) REVERT: A 303 MET cc_start: 0.8722 (ttp) cc_final: 0.8473 (ttp) REVERT: A 631 GLU cc_start: 0.8312 (pp20) cc_final: 0.7908 (pp20) REVERT: A 1031 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8381 (mm-30) REVERT: A 1128 MET cc_start: 0.8673 (tpp) cc_final: 0.8389 (tpt) REVERT: B 64 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8653 (pp20) REVERT: B 67 MET cc_start: 0.8302 (mmm) cc_final: 0.7765 (mmm) REVERT: B 159 ASN cc_start: 0.9043 (OUTLIER) cc_final: 0.8508 (p0) REVERT: B 575 MET cc_start: 0.9272 (mpp) cc_final: 0.8998 (mpt) REVERT: C 250 MET cc_start: 0.8995 (mmm) cc_final: 0.8739 (mmp) REVERT: E 18 GLU cc_start: 0.8963 (tp30) cc_final: 0.8352 (tp30) REVERT: E 67 SER cc_start: 0.9237 (p) cc_final: 0.9028 (p) REVERT: E 86 SER cc_start: 0.9461 (m) cc_final: 0.9199 (p) REVERT: E 144 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7956 (pm20) REVERT: G 86 ARG cc_start: 0.7895 (mtp180) cc_final: 0.7396 (tpt-90) REVERT: G 100 GLN cc_start: 0.8898 (mt0) cc_final: 0.8507 (mp10) REVERT: G 107 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8716 (mtmt) REVERT: G 110 ARG cc_start: 0.7398 (mmm160) cc_final: 0.7012 (tpm-80) REVERT: G 124 PHE cc_start: 0.7982 (m-80) cc_final: 0.7719 (m-80) REVERT: G 131 TYR cc_start: 0.6779 (m-80) cc_final: 0.6399 (m-80) REVERT: I 205 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8580 (ptpp) REVERT: I 281 TYR cc_start: 0.8557 (t80) cc_final: 0.8284 (t80) REVERT: I 486 LYS cc_start: 0.8646 (mttt) cc_final: 0.8304 (ptpp) REVERT: I 643 LYS cc_start: 0.9380 (OUTLIER) cc_final: 0.9118 (tptp) REVERT: J 51 GLN cc_start: 0.8445 (tp40) cc_final: 0.8002 (tp40) REVERT: S 104 CYS cc_start: 0.9210 (m) cc_final: 0.8470 (p) REVERT: S 141 ASP cc_start: 0.8220 (t0) cc_final: 0.7960 (t0) outliers start: 69 outliers final: 49 residues processed: 263 average time/residue: 1.4599 time to fit residues: 459.4430 Evaluate side-chains 258 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 202 time to evaluate : 3.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 92 HIS Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 547 ASP Chi-restraints excluded: chain I residue 558 SER Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 638 THR Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain I residue 666 THR Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 105 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 235 optimal weight: 0.7980 chunk 378 optimal weight: 6.9990 chunk 231 optimal weight: 4.9990 chunk 179 optimal weight: 0.0370 chunk 263 optimal weight: 5.9990 chunk 397 optimal weight: 0.1980 chunk 365 optimal weight: 10.0000 chunk 316 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 194 optimal weight: 0.3980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 HIS ** I 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 444 ASN I 567 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.089 33391 Z= 0.161 Angle : 0.546 12.785 45146 Z= 0.278 Chirality : 0.042 0.166 5114 Planarity : 0.003 0.049 5712 Dihedral : 5.120 83.581 4430 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.35 % Allowed : 13.34 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % 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: 0.33 (0.14), residues: 3991 helix: 1.30 (0.14), residues: 1499 sheet: 0.09 (0.24), residues: 511 loop : -0.54 (0.15), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 365 HIS 0.018 0.001 HIS I 197 PHE 0.028 0.001 PHE A 938 TYR 0.026 0.001 TYR A 264 ARG 0.013 0.000 ARG G 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 226 time to evaluate : 3.923 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 261 ASN cc_start: 0.9099 (OUTLIER) cc_final: 0.8892 (p0) REVERT: A 303 MET cc_start: 0.8697 (ttp) cc_final: 0.8486 (ttp) REVERT: A 631 GLU cc_start: 0.8307 (pp20) cc_final: 0.7867 (pp20) REVERT: A 1031 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8377 (mm-30) REVERT: A 1128 MET cc_start: 0.8650 (tpp) cc_final: 0.8355 (tpt) REVERT: B 64 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8724 (pp20) REVERT: B 67 MET cc_start: 0.8261 (mmm) cc_final: 0.7769 (mmm) REVERT: B 159 ASN cc_start: 0.9043 (OUTLIER) cc_final: 0.8471 (p0) REVERT: B 575 MET cc_start: 0.9261 (mpp) cc_final: 0.8726 (mpt) REVERT: E 18 GLU cc_start: 0.8970 (tp30) cc_final: 0.8324 (tp30) REVERT: E 67 SER cc_start: 0.9198 (p) cc_final: 0.8981 (p) REVERT: E 86 SER cc_start: 0.9454 (m) cc_final: 0.9214 (p) REVERT: E 144 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7959 (pm20) REVERT: G 86 ARG cc_start: 0.7916 (mtp180) cc_final: 0.7492 (tpt-90) REVERT: G 100 GLN cc_start: 0.8878 (mt0) cc_final: 0.8494 (mp10) REVERT: G 110 ARG cc_start: 0.7394 (mmm160) cc_final: 0.6989 (tpm-80) REVERT: G 124 PHE cc_start: 0.7930 (m-80) cc_final: 0.7705 (m-80) REVERT: G 131 TYR cc_start: 0.6790 (m-80) cc_final: 0.6399 (m-80) REVERT: I 205 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8624 (ptpp) REVERT: I 281 TYR cc_start: 0.8531 (t80) cc_final: 0.8267 (t80) REVERT: I 560 MET cc_start: 0.8189 (ptp) cc_final: 0.7900 (ttp) REVERT: I 643 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.9108 (tptp) REVERT: J 51 GLN cc_start: 0.8423 (tp40) cc_final: 0.8077 (tp40) REVERT: S 104 CYS cc_start: 0.9082 (m) cc_final: 0.8405 (p) REVERT: S 141 ASP cc_start: 0.8194 (t0) cc_final: 0.7956 (t0) outliers start: 50 outliers final: 31 residues processed: 266 average time/residue: 1.4776 time to fit residues: 470.6813 Evaluate side-chains 251 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 214 time to evaluate : 3.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 92 HIS Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 558 SER Chi-restraints excluded: chain I residue 638 THR Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain I residue 666 THR Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 105 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 251 optimal weight: 0.2980 chunk 337 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 291 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 317 optimal weight: 4.9990 chunk 132 optimal weight: 0.0370 chunk 325 optimal weight: 0.3980 chunk 40 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 GLN ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 HIS ** I 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 444 ASN I 567 HIS S 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.062839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.047547 restraints weight = 104084.400| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 3.12 r_work: 0.2657 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 33391 Z= 0.150 Angle : 0.542 15.039 45146 Z= 0.274 Chirality : 0.042 0.180 5114 Planarity : 0.003 0.067 5712 Dihedral : 4.979 82.715 4430 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.27 % Allowed : 13.77 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % 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: 0.41 (0.14), residues: 3991 helix: 1.39 (0.14), residues: 1487 sheet: 0.08 (0.24), residues: 514 loop : -0.50 (0.15), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1054 HIS 0.006 0.001 HIS I 197 PHE 0.028 0.001 PHE A 938 TYR 0.034 0.001 TYR S 134 ARG 0.017 0.000 ARG C 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9116.00 seconds wall clock time: 165 minutes 40.26 seconds (9940.26 seconds total)