Starting phenix.real_space_refine on Tue Feb 20 13:15:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4g_31450/02_2024/7f4g_31450.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4g_31450/02_2024/7f4g_31450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4g_31450/02_2024/7f4g_31450.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4g_31450/02_2024/7f4g_31450.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4g_31450/02_2024/7f4g_31450.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4g_31450/02_2024/7f4g_31450.pdb" } resolution = 2.78 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= -0.003 sd= 0.111 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: 5 Type Number sf(0) Gaussians Zn 5 6.06 5 S 162 5.16 5 C 17703 2.51 5 N 4833 2.21 5 O 5254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 500": "OE1" <-> "OE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A ARG 734": "NH1" <-> "NH2" Residue "A PHE 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 818": "OE1" <-> "OE2" Residue "A GLU 856": "OE1" <-> "OE2" Residue "A GLU 951": "OE1" <-> "OE2" Residue "A GLU 953": "OE1" <-> "OE2" Residue "A GLU 1057": "OE1" <-> "OE2" Residue "A GLU 1097": "OE1" <-> "OE2" Residue "A GLU 1126": "OE1" <-> "OE2" Residue "A ARG 1149": "NH1" <-> "NH2" Residue "A GLU 1215": "OE1" <-> "OE2" Residue "A GLU 1253": "OE1" <-> "OE2" Residue "A GLU 1266": "OE1" <-> "OE2" Residue "A GLU 1273": "OE1" <-> "OE2" Residue "A GLU 1381": "OE1" <-> "OE2" Residue "A ARG 1408": "NH1" <-> "NH2" Residue "A GLU 1478": "OE1" <-> "OE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "B GLU 816": "OE1" <-> "OE2" Residue "B GLU 959": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C ARG 160": "NH1" <-> "NH2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "E GLU 38": "OE1" <-> "OE2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E GLU 141": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E ARG 181": "NH1" <-> "NH2" Residue "F ARG 100": "NH1" <-> "NH2" Residue "F TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F GLU 122": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "J GLU 28": "OE1" <-> "OE2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 57": "OE1" <-> "OE2" Residue "K GLU 14": "OE1" <-> "OE2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K GLU 102": "OE1" <-> "OE2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L ARG 35": "NH1" <-> "NH2" Residue "R GLU 67": "OE1" <-> "OE2" Residue "R GLU 93": "OE1" <-> "OE2" Residue "R GLU 201": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "G GLU 8": "OE1" <-> "OE2" Residue "G TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 116": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27957 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 8179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8179 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 982} Chain breaks: 6 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 7820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7820 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 45, 'TRANS': 932} Chain breaks: 5 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2038 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 15, 'TRANS': 238} Chain breaks: 1 Chain: "E" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 11, 'TRANS': 196} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 609 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 524 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "R" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "D" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1005 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "G" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1334 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" 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 21582 SG CYS I 17 37.971 100.229 138.807 1.00 88.60 S ATOM 21606 SG CYS I 20 41.791 100.886 137.557 1.00 90.53 S ATOM 21767 SG CYS I 39 41.159 97.743 138.696 1.00 96.96 S ATOM 21792 SG CYS I 42 41.465 100.917 140.979 1.00101.32 S ATOM 22144 SG CYS I 86 10.786 98.574 103.888 1.00 86.89 S ATOM 22168 SG CYS I 89 9.770 101.931 103.105 1.00 88.50 S ATOM 22372 SG CYS I 114 12.931 100.997 101.748 1.00 73.84 S ATOM 22407 SG CYS I 119 12.341 101.481 105.283 1.00 84.48 S ATOM 22517 SG CYS J 7 51.508 98.144 40.982 1.00 32.48 S ATOM 22541 SG CYS J 10 50.924 97.140 37.600 1.00 36.95 S ATOM 22805 SG CYS J 44 48.463 96.157 40.502 1.00 40.01 S ATOM 22811 SG CYS J 45 48.849 99.419 38.764 1.00 40.13 S ATOM 24769 SG CYS R 100 63.096 54.764 141.450 1.00173.07 S ATOM 24806 SG CYS R 105 62.977 53.749 145.282 1.00177.93 S ATOM 25063 SG CYS R 136 59.838 54.641 144.515 1.00172.29 S ATOM 25094 SG CYS R 140 62.843 57.228 144.642 1.00175.77 S Time building chain proxies: 13.88, per 1000 atoms: 0.50 Number of scatterers: 27957 At special positions: 0 Unit cell: (170.172, 146.16, 161.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 5 29.99 S 162 16.00 O 5254 8.00 N 4833 7.00 C 17703 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 94 " distance=2.03 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: 9.55 Conformation dependent library (CDL) restraints added in 4.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN R 800 " pdb="ZN ZN R 800 " - pdb=" SG CYS R 140 " pdb="ZN ZN R 800 " - pdb=" SG CYS R 105 " pdb="ZN ZN R 800 " - pdb=" SG CYS R 100 " pdb="ZN ZN R 800 " - pdb=" SG CYS R 136 " Number of angles added : 24 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6604 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 40 sheets defined 36.7% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 508 through 519 removed outlier: 3.642A pdb=" N ARG A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 549 removed outlier: 3.947A pdb=" N ALA A 544 " --> pdb=" O ASP A 540 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL A 545 " --> pdb=" O THR A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 removed outlier: 3.593A pdb=" N ILE A 655 " --> pdb=" O SER A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 684 removed outlier: 3.652A pdb=" N ARG A 666 " --> pdb=" O HIS A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 733 through 758 Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.961A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 816 through 821 removed outlier: 3.529A pdb=" N ARG A 820 " --> pdb=" O GLY A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 868 removed outlier: 3.708A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 847 " --> pdb=" O GLY A 843 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 914 through 921 Processing helix chain 'A' and resid 935 through 944 removed outlier: 3.567A pdb=" N LEU A 943 " --> pdb=" O VAL A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 970 Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.712A pdb=" N TRP A 988 " --> pdb=" O LEU A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1017 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 removed outlier: 3.561A pdb=" N ASN A1042 " --> pdb=" O THR A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1057 Processing helix chain 'A' and resid 1061 through 1078 removed outlier: 3.541A pdb=" N ASP A1066 " --> pdb=" O GLY A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1119 through 1129 removed outlier: 3.997A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1189 through 1198 removed outlier: 3.574A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1224 removed outlier: 3.508A pdb=" N ARG A1224 " --> pdb=" O HIS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1239 Processing helix chain 'A' and resid 1280 through 1292 Processing helix chain 'A' and resid 1342 through 1347 Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.615A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1481 removed outlier: 3.791A pdb=" N LYS A1481 " --> pdb=" O ALA A1477 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 4.129A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 30 " --> pdb=" O CYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 60 removed outlier: 5.295A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 281 through 286 Processing helix chain 'B' and resid 294 through 302 removed outlier: 3.578A pdb=" N GLU B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 360 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 426 removed outlier: 3.926A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 579 through 592 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.720A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 658 Processing helix chain 'B' and resid 668 through 672 removed outlier: 3.643A pdb=" N GLU B 671 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 683 removed outlier: 3.593A pdb=" N GLN B 683 " --> pdb=" O PRO B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.789A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.614A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.523A pdb=" N GLU B 765 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.535A pdb=" N MET B 954 " --> pdb=" O GLN B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 976 Proline residue: B 973 - end of helix Processing helix chain 'B' and resid 977 through 994 removed outlier: 4.257A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1016 Processing helix chain 'C' and resid 27 through 41 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.512A pdb=" N GLU C 202 " --> pdb=" O LYS C 199 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP C 203 " --> pdb=" O PRO C 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 199 through 203' Processing helix chain 'C' and resid 240 through 268 removed outlier: 3.540A pdb=" N ILE C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 24 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 83 through 96 removed outlier: 3.949A pdb=" N GLU E 96 " --> pdb=" O GLN E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 99 No H-bonds generated for 'chain 'E' and resid 97 through 99' Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 removed outlier: 3.513A pdb=" N PHE E 183 " --> pdb=" O VAL E 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 4.056A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.815A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.930A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'R' and resid 43 through 66 Processing helix chain 'R' and resid 71 through 80 Processing helix chain 'R' and resid 83 through 97 Processing helix chain 'R' and resid 131 through 135 Processing helix chain 'R' and resid 137 through 150 Processing helix chain 'R' and resid 155 through 159 Processing helix chain 'R' and resid 162 through 183 removed outlier: 3.548A pdb=" N ASP R 166 " --> pdb=" O GLU R 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 removed outlier: 3.515A pdb=" N VAL D 37 " --> pdb=" O LEU D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.744A pdb=" N CYS D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 removed outlier: 3.722A pdb=" N GLU D 119 " --> pdb=" O PRO D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 123 through 137 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.694A pdb=" N GLU G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing sheet with id=AA1, first strand: chain 'A' and resid 367 through 369 Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.638A pdb=" N LYS A 445 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE A 419 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLU A 447 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.207A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE H 9 " --> pdb=" O GLU H 33 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.207A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AA6, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.765A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 902 through 904 Processing sheet with id=AA8, first strand: chain 'A' and resid 1140 through 1142 Processing sheet with id=AA9, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.895A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AB2, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AB3, first strand: chain 'B' and resid 91 through 93 removed outlier: 5.935A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AB5, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AB6, first strand: chain 'B' and resid 391 through 394 removed outlier: 3.609A pdb=" N LYS B 524 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 206 through 208 removed outlier: 6.823A pdb=" N MET B 239 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N THR B 218 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL B 237 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU B 220 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE B 235 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ARG B 222 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N SER B 233 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AB9, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AC1, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.671A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 748 through 751 removed outlier: 4.201A pdb=" N LYS B 917 " --> pdb=" O GLU B 818 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 748 through 751 removed outlier: 4.201A pdb=" N LYS B 917 " --> pdb=" O GLU B 818 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AC5, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.178A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ILE B 965 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE B 779 " --> pdb=" O ILE B 965 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE B 967 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA B 781 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AC7, first strand: chain 'B' and resid 865 through 867 removed outlier: 6.469A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 956 through 957 Processing sheet with id=AC9, first strand: chain 'C' and resid 8 through 15 removed outlier: 6.258A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE C 21 " --> pdb=" O TYR C 231 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.309A pdb=" N GLU C 158 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA C 54 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ARG C 160 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE C 52 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ARG C 162 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL C 50 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR C 164 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AD3, first strand: chain 'E' and resid 60 through 63 Processing sheet with id=AD4, first strand: chain 'E' and resid 104 through 106 removed outlier: 6.236A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'E' and resid 147 through 151 removed outlier: 4.913A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AD7, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AD8, first strand: chain 'K' and resid 20 through 24 removed outlier: 4.606A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 117 through 120 removed outlier: 3.606A pdb=" N LYS R 125 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 3 through 13 removed outlier: 3.584A pdb=" N THR G 39 " --> pdb=" O GLY G 43 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 3 through 13 Processing sheet with id=AE3, first strand: chain 'G' and resid 169 through 170 removed outlier: 3.685A pdb=" N GLY G 169 " --> pdb=" O ARG G 144 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY G 161 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 118 through 120 removed outlier: 3.992A pdb=" N TYR G 128 " --> pdb=" O ILE G 137 " (cutoff:3.500A) 1168 hydrogen bonds defined for protein. 3237 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: 11.53 Time building geometry restraints manager: 10.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4766 1.29 - 1.42: 7014 1.42 - 1.55: 16449 1.55 - 1.68: 1 1.68 - 1.81: 254 Bond restraints: 28484 Sorted by residual: bond pdb=" C LEU J 24 " pdb=" O LEU J 24 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.34e-02 5.57e+03 2.87e+01 bond pdb=" CA SER B 304 " pdb=" CB SER B 304 " ideal model delta sigma weight residual 1.537 1.466 0.071 1.41e-02 5.03e+03 2.55e+01 bond pdb=" N HIS B 842 " pdb=" CA HIS B 842 " ideal model delta sigma weight residual 1.457 1.489 -0.032 6.40e-03 2.44e+04 2.50e+01 bond pdb=" C LEU B 348 " pdb=" O LEU B 348 " ideal model delta sigma weight residual 1.235 1.212 0.023 4.70e-03 4.53e+04 2.34e+01 bond pdb=" C LYS B 302 " pdb=" O LYS B 302 " ideal model delta sigma weight residual 1.241 1.194 0.047 9.80e-03 1.04e+04 2.33e+01 ... (remaining 28479 not shown) Histogram of bond angle deviations from ideal: 95.62 - 103.55: 431 103.55 - 111.49: 12508 111.49 - 119.43: 11645 119.43 - 127.36: 13615 127.36 - 135.30: 278 Bond angle restraints: 38477 Sorted by residual: angle pdb=" C ILE B 556 " pdb=" N SER B 557 " pdb=" CA SER B 557 " ideal model delta sigma weight residual 121.83 135.30 -13.47 1.56e+00 4.11e-01 7.46e+01 angle pdb=" N LEU B 305 " pdb=" CA LEU B 305 " pdb=" C LEU B 305 " ideal model delta sigma weight residual 113.02 104.49 8.53 1.20e+00 6.94e-01 5.05e+01 angle pdb=" C PRO B 303 " pdb=" CA PRO B 303 " pdb=" CB PRO B 303 " ideal model delta sigma weight residual 111.56 100.76 10.80 1.65e+00 3.67e-01 4.29e+01 angle pdb=" N VAL B 742 " pdb=" CA VAL B 742 " pdb=" C VAL B 742 " ideal model delta sigma weight residual 113.71 107.61 6.10 9.50e-01 1.11e+00 4.12e+01 angle pdb=" CA THR B 898 " pdb=" C THR B 898 " pdb=" O THR B 898 " ideal model delta sigma weight residual 122.27 115.25 7.02 1.16e+00 7.43e-01 3.66e+01 ... (remaining 38472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15585 17.99 - 35.97: 1534 35.97 - 53.96: 265 53.96 - 71.94: 45 71.94 - 89.93: 23 Dihedral angle restraints: 17452 sinusoidal: 7260 harmonic: 10192 Sorted by residual: dihedral pdb=" CA GLY B 940 " pdb=" C GLY B 940 " pdb=" N GLN B 941 " pdb=" CA GLN B 941 " ideal model delta harmonic sigma weight residual 180.00 150.06 29.94 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ASP A1295 " pdb=" C ASP A1295 " pdb=" N MET A1296 " pdb=" CA MET A1296 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ARG C 240 " pdb=" C ARG C 240 " pdb=" N PRO C 241 " pdb=" CA PRO C 241 " ideal model delta harmonic sigma weight residual -180.00 -153.11 -26.89 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 17449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 3916 0.110 - 0.221: 369 0.221 - 0.331: 12 0.331 - 0.442: 6 0.442 - 0.552: 1 Chirality restraints: 4304 Sorted by residual: chirality pdb=" CB ILE A 811 " pdb=" CA ILE A 811 " pdb=" CG1 ILE A 811 " pdb=" CG2 ILE A 811 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.55 2.00e-01 2.50e+01 7.63e+00 chirality pdb=" CA TYR J 29 " pdb=" N TYR J 29 " pdb=" C TYR J 29 " pdb=" CB TYR J 29 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA ASN B 164 " pdb=" N ASN B 164 " pdb=" C ASN B 164 " pdb=" CB ASN B 164 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.81e+00 ... (remaining 4301 not shown) Planarity restraints: 4983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 388 " 0.035 2.00e-02 2.50e+03 2.81e-02 1.58e+01 pdb=" CG TYR B 388 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR B 388 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 388 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 388 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 388 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR B 388 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 388 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 752 " 0.014 2.00e-02 2.50e+03 2.26e-02 1.03e+01 pdb=" CG TYR B 752 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR B 752 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR B 752 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 752 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 752 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 752 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR B 752 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 668 " -0.018 2.00e-02 2.50e+03 2.29e-02 9.14e+00 pdb=" CG PHE A 668 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE A 668 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A 668 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 668 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 668 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 668 " 0.002 2.00e-02 2.50e+03 ... (remaining 4980 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 193 2.50 - 3.10: 20892 3.10 - 3.70: 42043 3.70 - 4.30: 64924 4.30 - 4.90: 109894 Nonbonded interactions: 237946 Sorted by model distance: nonbonded pdb=" O GLU L 38 " pdb="ZN ZN L 101 " model vdw 1.898 2.230 nonbonded pdb=" NE2 HIS B 387 " pdb=" OE2 GLU B 671 " model vdw 2.047 2.520 nonbonded pdb=" OD1 ASP B 953 " pdb=" NH2 ARG C 36 " model vdw 2.069 2.520 nonbonded pdb=" O ASN C 190 " pdb=" NH1 ARG C 193 " model vdw 2.089 2.520 nonbonded pdb=" OG SER R 95 " pdb=" OG SER R 134 " model vdw 2.090 2.440 ... (remaining 237941 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.450 Check model and map are aligned: 0.410 Set scattering table: 0.270 Process input model: 75.320 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:11.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.017 0.127 28484 Z= 1.103 Angle : 1.109 13.471 38477 Z= 0.631 Chirality : 0.067 0.552 4304 Planarity : 0.006 0.071 4983 Dihedral : 14.672 89.931 10845 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.69 % Favored : 90.96 % Rotamer: Outliers : 1.43 % Allowed : 6.48 % Favored : 92.10 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.63 % 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: -3.97 (0.12), residues: 3441 helix: -2.63 (0.11), residues: 1201 sheet: -2.51 (0.20), residues: 487 loop : -2.66 (0.13), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP C 49 HIS 0.011 0.002 HIS B 749 PHE 0.051 0.004 PHE A 668 TYR 0.067 0.004 TYR B 388 ARG 0.013 0.001 ARG A1258 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 523 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 HIS cc_start: 0.7388 (t70) cc_final: 0.6140 (m90) REVERT: A 540 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6531 (m-30) REVERT: A 660 MET cc_start: 0.8092 (mmm) cc_final: 0.7850 (mmp) REVERT: A 701 ASP cc_start: 0.7730 (t70) cc_final: 0.7476 (t0) REVERT: A 711 GLN cc_start: 0.7114 (mt0) cc_final: 0.6791 (tm-30) REVERT: A 811 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8006 (pt) REVERT: A 859 TYR cc_start: 0.7869 (t80) cc_final: 0.7604 (t80) REVERT: A 947 HIS cc_start: 0.7305 (t70) cc_final: 0.6812 (t70) REVERT: A 951 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6740 (mt-10) REVERT: A 955 GLU cc_start: 0.7656 (tt0) cc_final: 0.7242 (tt0) REVERT: A 959 MET cc_start: 0.8457 (ttm) cc_final: 0.8188 (mtp) REVERT: A 1031 ARG cc_start: 0.7426 (mtt180) cc_final: 0.7171 (mtt90) REVERT: A 1146 GLN cc_start: 0.8389 (mp10) cc_final: 0.7784 (tp-100) REVERT: A 1230 GLN cc_start: 0.9030 (mt0) cc_final: 0.8800 (mt0) REVERT: A 1233 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7946 (mm-30) REVERT: A 1280 ASP cc_start: 0.7948 (m-30) cc_final: 0.7746 (m-30) REVERT: A 1289 GLU cc_start: 0.6723 (tm-30) cc_final: 0.6491 (tp30) REVERT: A 1293 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7136 (tt) REVERT: A 1376 LYS cc_start: 0.8223 (tptt) cc_final: 0.8022 (tppp) REVERT: B 61 ASP cc_start: 0.7094 (m-30) cc_final: 0.6728 (m-30) REVERT: B 92 TYR cc_start: 0.7594 (m-80) cc_final: 0.7015 (m-80) REVERT: B 281 ASP cc_start: 0.8615 (t0) cc_final: 0.8186 (t0) REVERT: B 606 ASP cc_start: 0.7165 (m-30) cc_final: 0.6814 (m-30) REVERT: B 632 LYS cc_start: 0.8260 (mttt) cc_final: 0.8055 (mttp) REVERT: C 3 TYR cc_start: 0.8390 (m-80) cc_final: 0.8185 (m-10) REVERT: C 260 GLN cc_start: 0.8372 (tp40) cc_final: 0.8010 (tt0) REVERT: E 79 GLU cc_start: 0.8506 (mp0) cc_final: 0.7989 (mp0) REVERT: E 117 SER cc_start: 0.8751 (t) cc_final: 0.8434 (t) REVERT: E 168 ASN cc_start: 0.8436 (p0) cc_final: 0.8066 (p0) REVERT: F 101 LYS cc_start: 0.8572 (mttp) cc_final: 0.8354 (mttm) REVERT: H 51 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7638 (p0) REVERT: H 54 ASP cc_start: 0.7953 (m-30) cc_final: 0.7698 (m-30) REVERT: H 57 ARG cc_start: 0.8064 (ttt-90) cc_final: 0.7838 (ttt180) REVERT: H 89 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8158 (mt-10) REVERT: H 146 LYS cc_start: 0.8442 (tttp) cc_final: 0.8214 (ttpt) REVERT: I 67 GLN cc_start: 0.8742 (mm110) cc_final: 0.8461 (mp10) REVERT: I 93 GLU cc_start: 0.8313 (tt0) cc_final: 0.7932 (tt0) REVERT: K 38 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7352 (mm-30) REVERT: K 70 LYS cc_start: 0.8738 (ptpt) cc_final: 0.8505 (ptpp) REVERT: L 42 ARG cc_start: 0.8221 (mtt-85) cc_final: 0.7900 (mtp85) REVERT: L 51 ARG cc_start: 0.8266 (ttm110) cc_final: 0.8062 (ttm170) REVERT: D 62 MET cc_start: 0.3194 (mmp) cc_final: 0.2733 (mmp) REVERT: G 164 MET cc_start: 0.0910 (mmt) cc_final: 0.0239 (pp-130) outliers start: 44 outliers final: 13 residues processed: 560 average time/residue: 1.6297 time to fit residues: 1042.3735 Evaluate side-chains 420 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 403 time to evaluate : 3.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 43 ASP Chi-restraints excluded: chain J residue 5 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 0.9990 chunk 259 optimal weight: 0.8980 chunk 143 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 268 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 162 optimal weight: 0.7980 chunk 199 optimal weight: 2.9990 chunk 310 optimal weight: 40.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN A 432 HIS A 504 HIS ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS A 671 ASN A 678 ASN A 711 GLN A 721 HIS A 735 GLN ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 GLN A 839 HIS A 885 GLN A 949 GLN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 GLN A1230 GLN A1291 ASN A1332 GLN A1397 HIS B 56 GLN B 117 ASN B 265 GLN B 471 ASN B 500 GLN B 552 ASN B 582 GLN B 639 HIS B 649 ASN B 650 ASN B 654 GLN B 699 HIS ** B 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 HIS ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 108 ASN C 260 GLN C 265 HIS E 19 GLN E 64 HIS ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN E 108 GLN I 41 ASN I 67 GLN I 84 HIS J 52 HIS K 22 ASN K 29 ASN K 69 HIS ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN R 64 GLN R 86 HIS R 138 ASN R 199 HIS D 89 GLN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28484 Z= 0.243 Angle : 0.672 15.841 38477 Z= 0.347 Chirality : 0.047 0.231 4304 Planarity : 0.005 0.060 4983 Dihedral : 6.247 56.875 3832 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.22 % Favored : 93.69 % Rotamer: Outliers : 3.50 % Allowed : 13.74 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: -2.56 (0.13), residues: 3441 helix: -1.10 (0.14), residues: 1212 sheet: -2.06 (0.21), residues: 480 loop : -2.00 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 679 HIS 0.010 0.001 HIS C 265 PHE 0.026 0.002 PHE A 592 TYR 0.026 0.002 TYR B 388 ARG 0.009 0.001 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 430 time to evaluate : 3.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 HIS cc_start: 0.7234 (t-90) cc_final: 0.6143 (m90) REVERT: A 508 SER cc_start: 0.8136 (OUTLIER) cc_final: 0.7825 (t) REVERT: A 540 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6770 (m-30) REVERT: A 637 MET cc_start: 0.8882 (ptm) cc_final: 0.8584 (ptp) REVERT: A 660 MET cc_start: 0.7848 (mmm) cc_final: 0.7603 (mmp) REVERT: A 859 TYR cc_start: 0.7777 (t80) cc_final: 0.7526 (t80) REVERT: A 868 MET cc_start: 0.6992 (mtm) cc_final: 0.6592 (mtm) REVERT: A 927 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: A 951 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6908 (mt-10) REVERT: A 955 GLU cc_start: 0.7478 (tt0) cc_final: 0.7152 (tt0) REVERT: A 1152 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7617 (pt0) REVERT: A 1230 GLN cc_start: 0.8986 (mt0) cc_final: 0.8745 (mt0) REVERT: A 1233 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7985 (mm-30) REVERT: A 1279 MET cc_start: 0.7806 (mtp) cc_final: 0.7583 (mtm) REVERT: A 1408 ARG cc_start: 0.7841 (mmm160) cc_final: 0.7580 (mmm160) REVERT: B 92 TYR cc_start: 0.7549 (m-80) cc_final: 0.6957 (m-80) REVERT: B 151 LYS cc_start: 0.7866 (mtpp) cc_final: 0.7611 (mtmt) REVERT: B 155 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8581 (ttm) REVERT: B 160 TYR cc_start: 0.7829 (m-80) cc_final: 0.7494 (m-80) REVERT: B 222 ARG cc_start: 0.8143 (mtt-85) cc_final: 0.7674 (mtt90) REVERT: B 265 GLN cc_start: 0.8359 (mt0) cc_final: 0.8112 (mm-40) REVERT: B 302 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.7948 (mtmt) REVERT: B 309 PHE cc_start: 0.8789 (t80) cc_final: 0.8454 (t80) REVERT: B 334 LYS cc_start: 0.7740 (tppp) cc_final: 0.7199 (ttpp) REVERT: B 450 THR cc_start: 0.8721 (m) cc_final: 0.8483 (p) REVERT: B 529 MET cc_start: 0.9028 (mtp) cc_final: 0.8666 (mtt) REVERT: B 721 ARG cc_start: 0.8855 (mmp80) cc_final: 0.8536 (mmp80) REVERT: B 745 ASP cc_start: 0.7654 (m-30) cc_final: 0.7417 (m-30) REVERT: B 764 MET cc_start: 0.8598 (mtt) cc_final: 0.8308 (mtm) REVERT: B 965 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8471 (mm) REVERT: C 3 TYR cc_start: 0.8077 (m-80) cc_final: 0.7792 (m-80) REVERT: C 17 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7298 (pt0) REVERT: E 79 GLU cc_start: 0.8659 (mp0) cc_final: 0.8282 (mp0) REVERT: E 168 ASN cc_start: 0.8564 (p0) cc_final: 0.8332 (p0) REVERT: E 177 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7544 (t0) REVERT: H 20 LYS cc_start: 0.8842 (tttt) cc_final: 0.8530 (mtpt) REVERT: H 51 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7522 (p0) REVERT: H 54 ASP cc_start: 0.7803 (m-30) cc_final: 0.7445 (m-30) REVERT: H 57 ARG cc_start: 0.7967 (ttt-90) cc_final: 0.7566 (ttt180) REVERT: I 27 LYS cc_start: 0.7419 (ptpt) cc_final: 0.7161 (ptpp) REVERT: I 67 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8340 (mp10) REVERT: I 93 GLU cc_start: 0.8311 (tt0) cc_final: 0.7934 (tt0) REVERT: K 38 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7422 (mm-30) REVERT: L 15 MET cc_start: 0.7214 (tpp) cc_final: 0.7002 (tpp) REVERT: L 27 GLU cc_start: 0.7684 (tt0) cc_final: 0.7450 (tm-30) REVERT: L 42 ARG cc_start: 0.8032 (mtt-85) cc_final: 0.7731 (mtp85) REVERT: R 76 MET cc_start: 0.6406 (mmp) cc_final: 0.5872 (mmt) REVERT: G 1 MET cc_start: 0.4179 (pmm) cc_final: 0.3419 (ppp) outliers start: 108 outliers final: 39 residues processed: 491 average time/residue: 1.4517 time to fit residues: 825.5109 Evaluate side-chains 416 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 367 time to evaluate : 3.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1152 GLU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 131 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 172 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 258 optimal weight: 8.9990 chunk 211 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 311 optimal weight: 8.9990 chunk 336 optimal weight: 50.0000 chunk 277 optimal weight: 0.8980 chunk 308 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 249 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 GLN B 500 GLN B 582 GLN B 649 ASN B1025 ASN ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN H 126 GLN I 41 ASN ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 28484 Z= 0.315 Angle : 0.647 11.212 38477 Z= 0.331 Chirality : 0.047 0.190 4304 Planarity : 0.005 0.064 4983 Dihedral : 5.728 51.076 3819 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.99 % Favored : 93.96 % Rotamer: Outliers : 4.47 % Allowed : 15.68 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: -1.87 (0.14), residues: 3441 helix: -0.46 (0.14), residues: 1222 sheet: -1.61 (0.22), residues: 481 loop : -1.68 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 22 HIS 0.008 0.001 HIS A 662 PHE 0.025 0.002 PHE A 592 TYR 0.023 0.002 TYR B 388 ARG 0.009 0.001 ARG B 255 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 402 time to evaluate : 3.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 ASN cc_start: 0.8532 (p0) cc_final: 0.8227 (p0) REVERT: A 504 HIS cc_start: 0.7328 (t-90) cc_final: 0.6289 (m90) REVERT: A 508 SER cc_start: 0.8134 (m) cc_final: 0.7913 (p) REVERT: A 509 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7186 (tt) REVERT: A 637 MET cc_start: 0.8913 (ptm) cc_final: 0.8604 (ptp) REVERT: A 711 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.7162 (mt0) REVERT: A 859 TYR cc_start: 0.7787 (t80) cc_final: 0.7504 (t80) REVERT: A 862 ARG cc_start: 0.7918 (mtt90) cc_final: 0.7714 (mtm-85) REVERT: A 927 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7167 (tm-30) REVERT: A 951 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6848 (mt-10) REVERT: A 955 GLU cc_start: 0.7418 (tt0) cc_final: 0.7212 (tt0) REVERT: A 1015 GLU cc_start: 0.6985 (mp0) cc_final: 0.6753 (mp0) REVERT: A 1031 ARG cc_start: 0.7416 (mtt180) cc_final: 0.7186 (mtt90) REVERT: A 1102 MET cc_start: 0.6237 (mtp) cc_final: 0.5832 (mtm) REVERT: A 1152 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7628 (pt0) REVERT: A 1230 GLN cc_start: 0.8971 (mt0) cc_final: 0.8692 (mt0) REVERT: A 1233 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7961 (mm-30) REVERT: A 1271 GLU cc_start: 0.1818 (OUTLIER) cc_final: 0.0866 (mp0) REVERT: A 1279 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7631 (mtm) REVERT: A 1293 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7612 (tt) REVERT: A 1339 ASP cc_start: 0.7891 (t0) cc_final: 0.7322 (m-30) REVERT: A 1408 ARG cc_start: 0.7879 (mmm160) cc_final: 0.7565 (mmm160) REVERT: B 51 ILE cc_start: 0.8995 (tp) cc_final: 0.8621 (tp) REVERT: B 61 ASP cc_start: 0.7129 (m-30) cc_final: 0.6844 (m-30) REVERT: B 92 TYR cc_start: 0.7498 (m-80) cc_final: 0.6884 (m-80) REVERT: B 155 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8597 (ttm) REVERT: B 302 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.7882 (mtmt) REVERT: B 309 PHE cc_start: 0.8809 (t80) cc_final: 0.8508 (t80) REVERT: B 424 ASP cc_start: 0.6392 (OUTLIER) cc_final: 0.6114 (p0) REVERT: B 450 THR cc_start: 0.8750 (m) cc_final: 0.8538 (p) REVERT: B 508 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.7761 (mtt) REVERT: B 529 MET cc_start: 0.9050 (mtp) cc_final: 0.8792 (mtt) REVERT: B 721 ARG cc_start: 0.8762 (mmp80) cc_final: 0.8504 (mmp80) REVERT: B 764 MET cc_start: 0.8589 (mtt) cc_final: 0.8318 (mtm) REVERT: B 965 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8633 (mm) REVERT: C 3 TYR cc_start: 0.8032 (m-80) cc_final: 0.7779 (m-80) REVERT: C 17 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7372 (pm20) REVERT: E 79 GLU cc_start: 0.8746 (mp0) cc_final: 0.8139 (pm20) REVERT: H 20 LYS cc_start: 0.8858 (mttt) cc_final: 0.8542 (mtpt) REVERT: H 51 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7602 (p0) REVERT: H 54 ASP cc_start: 0.7725 (m-30) cc_final: 0.7247 (m-30) REVERT: H 57 ARG cc_start: 0.7920 (ttt-90) cc_final: 0.7561 (ttt180) REVERT: I 27 LYS cc_start: 0.7404 (ptpt) cc_final: 0.7121 (ptpp) REVERT: I 67 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8379 (mp10) REVERT: I 93 GLU cc_start: 0.8308 (tt0) cc_final: 0.7961 (tt0) REVERT: L 42 ARG cc_start: 0.8152 (mtt-85) cc_final: 0.7818 (mtp85) REVERT: R 104 LEU cc_start: 0.8626 (mm) cc_final: 0.8342 (mp) REVERT: G 1 MET cc_start: 0.4892 (pmm) cc_final: 0.3888 (ppp) outliers start: 138 outliers final: 60 residues processed: 486 average time/residue: 1.5093 time to fit residues: 848.5252 Evaluate side-chains 453 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 379 time to evaluate : 3.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1152 GLU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1303 GLN Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 849 ASP Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1026 GLU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 43 ASP Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 131 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 307 optimal weight: 5.9990 chunk 233 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 208 optimal weight: 0.9980 chunk 312 optimal weight: 8.9990 chunk 330 optimal weight: 6.9990 chunk 163 optimal weight: 0.5980 chunk 295 optimal weight: 0.0370 chunk 89 optimal weight: 10.0000 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN A 671 ASN ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN B 582 GLN B 941 GLN ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28484 Z= 0.200 Angle : 0.592 12.881 38477 Z= 0.301 Chirality : 0.045 0.170 4304 Planarity : 0.004 0.059 4983 Dihedral : 5.400 57.658 3817 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.52 % Favored : 94.39 % Rotamer: Outliers : 4.24 % Allowed : 17.43 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: -1.38 (0.14), residues: 3441 helix: -0.00 (0.15), residues: 1215 sheet: -1.36 (0.22), residues: 485 loop : -1.41 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 679 HIS 0.006 0.001 HIS R 177 PHE 0.021 0.001 PHE A 592 TYR 0.013 0.001 TYR B 388 ARG 0.009 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 411 time to evaluate : 3.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 ASN cc_start: 0.8366 (p0) cc_final: 0.8086 (p0) REVERT: A 504 HIS cc_start: 0.7391 (t-90) cc_final: 0.6309 (m90) REVERT: A 508 SER cc_start: 0.8090 (OUTLIER) cc_final: 0.7871 (p) REVERT: A 509 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7049 (tt) REVERT: A 520 MET cc_start: 0.7602 (mmm) cc_final: 0.7348 (mmm) REVERT: A 637 MET cc_start: 0.8838 (ptm) cc_final: 0.8578 (ptp) REVERT: A 711 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6996 (mt0) REVERT: A 803 LYS cc_start: 0.7795 (tppp) cc_final: 0.7355 (ttpp) REVERT: A 859 TYR cc_start: 0.7813 (t80) cc_final: 0.7499 (t80) REVERT: A 927 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7161 (tm-30) REVERT: A 947 HIS cc_start: 0.6881 (t70) cc_final: 0.6564 (t-170) REVERT: A 1015 GLU cc_start: 0.6888 (mp0) cc_final: 0.6632 (mp0) REVERT: A 1102 MET cc_start: 0.6299 (mtp) cc_final: 0.5906 (mtm) REVERT: A 1230 GLN cc_start: 0.9000 (mt0) cc_final: 0.8696 (mt0) REVERT: A 1233 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7993 (mm-30) REVERT: A 1269 MET cc_start: 0.1462 (pmm) cc_final: 0.1256 (tpt) REVERT: A 1279 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7595 (mtm) REVERT: A 1293 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7544 (tt) REVERT: A 1339 ASP cc_start: 0.7852 (t0) cc_final: 0.7284 (m-30) REVERT: A 1355 VAL cc_start: 0.8441 (m) cc_final: 0.8173 (t) REVERT: A 1408 ARG cc_start: 0.7829 (mmm160) cc_final: 0.7587 (mmm160) REVERT: B 61 ASP cc_start: 0.7428 (m-30) cc_final: 0.7193 (m-30) REVERT: B 92 TYR cc_start: 0.7446 (m-80) cc_final: 0.6834 (m-80) REVERT: B 155 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8526 (ttm) REVERT: B 170 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7704 (m-30) REVERT: B 302 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8014 (ttmt) REVERT: B 309 PHE cc_start: 0.8818 (t80) cc_final: 0.8560 (t80) REVERT: B 424 ASP cc_start: 0.6429 (OUTLIER) cc_final: 0.6164 (p0) REVERT: B 508 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.7673 (mtt) REVERT: B 529 MET cc_start: 0.9007 (mtp) cc_final: 0.8793 (mtt) REVERT: B 721 ARG cc_start: 0.8663 (mmp80) cc_final: 0.8396 (mmp80) REVERT: B 744 MET cc_start: 0.9074 (mtt) cc_final: 0.8736 (mtm) REVERT: B 764 MET cc_start: 0.8569 (mtm) cc_final: 0.8341 (mtm) REVERT: B 913 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7804 (mt0) REVERT: B 941 GLN cc_start: 0.6081 (tp40) cc_final: 0.5869 (tp40) REVERT: B 965 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8520 (mm) REVERT: C 126 ARG cc_start: 0.7392 (mtm180) cc_final: 0.7127 (ptm160) REVERT: E 55 ARG cc_start: 0.7479 (mmm-85) cc_final: 0.7193 (mmt90) REVERT: E 79 GLU cc_start: 0.8764 (mp0) cc_final: 0.8164 (pm20) REVERT: H 51 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7502 (p0) REVERT: H 54 ASP cc_start: 0.7707 (m-30) cc_final: 0.7193 (m-30) REVERT: I 27 LYS cc_start: 0.7329 (ptpt) cc_final: 0.7051 (ptpp) REVERT: I 51 SER cc_start: 0.7889 (t) cc_final: 0.7568 (p) REVERT: I 67 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8356 (mp10) REVERT: I 93 GLU cc_start: 0.8290 (tt0) cc_final: 0.7917 (tt0) REVERT: K 110 LYS cc_start: 0.8273 (ttmm) cc_final: 0.8035 (mtpp) REVERT: L 38 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.6482 (pp20) REVERT: L 42 ARG cc_start: 0.8153 (mtt-85) cc_final: 0.7847 (mtp85) REVERT: R 76 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.5957 (mmp) REVERT: D 33 LEU cc_start: 0.2051 (OUTLIER) cc_final: 0.1686 (mm) REVERT: D 39 MET cc_start: 0.2533 (OUTLIER) cc_final: 0.2307 (ptm) REVERT: G 1 MET cc_start: 0.5350 (pmm) cc_final: 0.4234 (ppp) outliers start: 131 outliers final: 51 residues processed: 496 average time/residue: 1.5466 time to fit residues: 909.2131 Evaluate side-chains 442 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 373 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 849 ASP Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain I residue 43 ASP Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 122 ARG Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 76 MET Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 119 ILE Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 131 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 275 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 246 optimal weight: 0.5980 chunk 136 optimal weight: 5.9990 chunk 282 optimal weight: 1.9990 chunk 228 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 296 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS B 582 GLN B 649 ASN B 749 HIS ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN E 108 GLN H 44 ASN K 84 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 28484 Z= 0.361 Angle : 0.637 12.353 38477 Z= 0.322 Chirality : 0.047 0.213 4304 Planarity : 0.004 0.060 4983 Dihedral : 5.419 58.015 3815 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.93 % Favored : 94.01 % Rotamer: Outliers : 4.92 % Allowed : 17.85 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: -1.23 (0.14), residues: 3441 helix: 0.12 (0.15), residues: 1216 sheet: -1.30 (0.22), residues: 488 loop : -1.31 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 27 HIS 0.006 0.001 HIS R 60 PHE 0.024 0.002 PHE A 592 TYR 0.016 0.002 TYR E 182 ARG 0.010 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 393 time to evaluate : 3.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 ASN cc_start: 0.8344 (p0) cc_final: 0.8044 (p0) REVERT: A 504 HIS cc_start: 0.7367 (t-90) cc_final: 0.6294 (m90) REVERT: A 508 SER cc_start: 0.8152 (OUTLIER) cc_final: 0.7898 (p) REVERT: A 509 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7119 (tt) REVERT: A 662 HIS cc_start: 0.6872 (OUTLIER) cc_final: 0.6570 (t-90) REVERT: A 711 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.6999 (mt0) REVERT: A 859 TYR cc_start: 0.7765 (t80) cc_final: 0.7472 (t80) REVERT: A 927 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7196 (tm-30) REVERT: A 947 HIS cc_start: 0.6905 (t70) cc_final: 0.6607 (t-170) REVERT: A 951 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6809 (mt-10) REVERT: A 1015 GLU cc_start: 0.6882 (mp0) cc_final: 0.6559 (mp0) REVERT: A 1031 ARG cc_start: 0.7419 (mtt180) cc_final: 0.7198 (mtt90) REVERT: A 1102 MET cc_start: 0.6394 (mtp) cc_final: 0.5996 (mtm) REVERT: A 1152 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7720 (pm20) REVERT: A 1230 GLN cc_start: 0.8996 (mt0) cc_final: 0.8757 (mt0) REVERT: A 1233 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8000 (mm-30) REVERT: A 1279 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7635 (mtm) REVERT: A 1293 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7414 (tt) REVERT: A 1339 ASP cc_start: 0.7970 (t0) cc_final: 0.7380 (m-30) REVERT: A 1355 VAL cc_start: 0.8446 (m) cc_final: 0.8173 (t) REVERT: A 1408 ARG cc_start: 0.7847 (mmm160) cc_final: 0.7643 (mmm160) REVERT: B 61 ASP cc_start: 0.7515 (m-30) cc_final: 0.7315 (m-30) REVERT: B 92 TYR cc_start: 0.7426 (m-80) cc_final: 0.6851 (m-80) REVERT: B 155 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8603 (ttm) REVERT: B 160 TYR cc_start: 0.7821 (m-80) cc_final: 0.7486 (m-80) REVERT: B 169 ARG cc_start: 0.7193 (mtp-110) cc_final: 0.6924 (ttt-90) REVERT: B 170 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7744 (m-30) REVERT: B 224 CYS cc_start: 0.7272 (p) cc_final: 0.7021 (p) REVERT: B 302 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.7888 (mtmt) REVERT: B 309 PHE cc_start: 0.8832 (t80) cc_final: 0.8570 (t80) REVERT: B 424 ASP cc_start: 0.6474 (OUTLIER) cc_final: 0.6235 (p0) REVERT: B 508 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.7794 (mtt) REVERT: B 529 MET cc_start: 0.9046 (mtp) cc_final: 0.8831 (mtt) REVERT: B 721 ARG cc_start: 0.8675 (mmp80) cc_final: 0.8418 (mmp80) REVERT: B 764 MET cc_start: 0.8593 (mtm) cc_final: 0.8305 (mtm) REVERT: B 913 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: B 941 GLN cc_start: 0.6163 (tp40) cc_final: 0.5877 (tp40) REVERT: B 965 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8670 (mm) REVERT: C 5 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.7938 (p0) REVERT: C 6 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7804 (mt0) REVERT: C 126 ARG cc_start: 0.7412 (mtm180) cc_final: 0.6889 (ptm160) REVERT: C 262 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: E 79 GLU cc_start: 0.8781 (mp0) cc_final: 0.8183 (pm20) REVERT: H 20 LYS cc_start: 0.8876 (mtpt) cc_final: 0.8627 (tptp) REVERT: H 51 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7560 (p0) REVERT: H 54 ASP cc_start: 0.7774 (m-30) cc_final: 0.7191 (m-30) REVERT: I 27 LYS cc_start: 0.7261 (ptpt) cc_final: 0.6952 (ptpp) REVERT: I 51 SER cc_start: 0.7836 (t) cc_final: 0.7551 (p) REVERT: I 67 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8376 (mp10) REVERT: I 93 GLU cc_start: 0.8288 (tt0) cc_final: 0.7916 (tt0) REVERT: K 110 LYS cc_start: 0.8274 (ttmm) cc_final: 0.8032 (mtpp) REVERT: L 42 ARG cc_start: 0.8206 (mtt-85) cc_final: 0.7928 (mtp85) REVERT: R 104 LEU cc_start: 0.8540 (mm) cc_final: 0.8029 (pp) REVERT: R 185 CYS cc_start: 0.5172 (OUTLIER) cc_final: 0.3804 (t) REVERT: R 189 ILE cc_start: 0.4051 (OUTLIER) cc_final: 0.2425 (mt) REVERT: D 33 LEU cc_start: 0.2031 (OUTLIER) cc_final: 0.1632 (mm) REVERT: D 39 MET cc_start: 0.2651 (OUTLIER) cc_final: 0.2434 (ptm) REVERT: G 1 MET cc_start: 0.5279 (OUTLIER) cc_final: 0.3957 (ppp) outliers start: 152 outliers final: 73 residues processed: 493 average time/residue: 1.4790 time to fit residues: 844.0632 Evaluate side-chains 472 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 375 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1152 GLU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 849 ASP Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain B residue 1026 GLU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 43 ASP Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 122 ARG Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 119 ILE Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 131 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 111 optimal weight: 8.9990 chunk 297 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 330 optimal weight: 4.9990 chunk 274 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN B 500 GLN B 582 GLN ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN H 44 ASN I 45 GLN R 115 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 28484 Z= 0.321 Angle : 0.631 15.050 38477 Z= 0.317 Chirality : 0.047 0.259 4304 Planarity : 0.004 0.061 4983 Dihedral : 5.364 57.395 3815 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.75 % Favored : 94.19 % Rotamer: Outliers : 4.54 % Allowed : 19.08 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: -1.05 (0.14), residues: 3441 helix: 0.27 (0.15), residues: 1209 sheet: -1.21 (0.22), residues: 487 loop : -1.20 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 49 HIS 0.006 0.001 HIS R 177 PHE 0.023 0.002 PHE A 592 TYR 0.019 0.001 TYR E 182 ARG 0.010 0.000 ARG B 770 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 396 time to evaluate : 3.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 ASN cc_start: 0.8315 (p0) cc_final: 0.8045 (OUTLIER) REVERT: A 504 HIS cc_start: 0.7399 (t-90) cc_final: 0.6263 (m90) REVERT: A 508 SER cc_start: 0.8157 (OUTLIER) cc_final: 0.7882 (p) REVERT: A 509 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7105 (tt) REVERT: A 637 MET cc_start: 0.8892 (ptm) cc_final: 0.8586 (ptp) REVERT: A 711 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.7057 (mt0) REVERT: A 769 MET cc_start: 0.7261 (mtt) cc_final: 0.6943 (mtt) REVERT: A 803 LYS cc_start: 0.7827 (tppp) cc_final: 0.7413 (ttpp) REVERT: A 859 TYR cc_start: 0.7762 (t80) cc_final: 0.7472 (t80) REVERT: A 866 LYS cc_start: 0.7979 (tmmt) cc_final: 0.7657 (pptt) REVERT: A 927 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7197 (tm-30) REVERT: A 947 HIS cc_start: 0.6878 (t70) cc_final: 0.6571 (t-170) REVERT: A 951 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6774 (mt-10) REVERT: A 1015 GLU cc_start: 0.6953 (mp0) cc_final: 0.6669 (mp0) REVERT: A 1031 ARG cc_start: 0.7417 (mtt180) cc_final: 0.7112 (mtt90) REVERT: A 1102 MET cc_start: 0.6329 (mtp) cc_final: 0.6046 (mtm) REVERT: A 1230 GLN cc_start: 0.8996 (mt0) cc_final: 0.8697 (mt0) REVERT: A 1233 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8002 (mm-30) REVERT: A 1269 MET cc_start: 0.1424 (pmm) cc_final: 0.1047 (tpt) REVERT: A 1271 GLU cc_start: 0.2247 (OUTLIER) cc_final: 0.1476 (mp0) REVERT: A 1279 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7652 (mtm) REVERT: A 1293 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7426 (tt) REVERT: A 1339 ASP cc_start: 0.7975 (t0) cc_final: 0.7396 (m-30) REVERT: A 1355 VAL cc_start: 0.8446 (m) cc_final: 0.8161 (t) REVERT: B 51 ILE cc_start: 0.8944 (tp) cc_final: 0.8661 (tp) REVERT: B 61 ASP cc_start: 0.7475 (m-30) cc_final: 0.7263 (m-30) REVERT: B 92 TYR cc_start: 0.7381 (m-80) cc_final: 0.6801 (m-80) REVERT: B 155 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8557 (ttm) REVERT: B 160 TYR cc_start: 0.7811 (m-80) cc_final: 0.7477 (m-80) REVERT: B 170 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7654 (m-30) REVERT: B 224 CYS cc_start: 0.7268 (p) cc_final: 0.7024 (p) REVERT: B 302 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.7889 (mtmt) REVERT: B 309 PHE cc_start: 0.8833 (t80) cc_final: 0.8570 (t80) REVERT: B 424 ASP cc_start: 0.6444 (OUTLIER) cc_final: 0.6194 (p0) REVERT: B 433 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7566 (pt) REVERT: B 452 ASN cc_start: 0.8496 (m-40) cc_final: 0.8277 (m-40) REVERT: B 529 MET cc_start: 0.9042 (mtp) cc_final: 0.8832 (mtt) REVERT: B 721 ARG cc_start: 0.8606 (mmp80) cc_final: 0.8391 (mmp80) REVERT: B 764 MET cc_start: 0.8584 (mtm) cc_final: 0.8343 (mtm) REVERT: B 913 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7779 (tt0) REVERT: B 941 GLN cc_start: 0.6137 (tp40) cc_final: 0.5811 (tp40) REVERT: B 965 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8651 (mm) REVERT: C 5 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.7928 (p0) REVERT: C 126 ARG cc_start: 0.7347 (mtm180) cc_final: 0.6890 (ptm160) REVERT: C 262 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7394 (mp10) REVERT: E 79 GLU cc_start: 0.8778 (mp0) cc_final: 0.8185 (pm20) REVERT: E 128 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7680 (pt0) REVERT: F 51 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6155 (mtp180) REVERT: H 51 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7492 (p0) REVERT: H 54 ASP cc_start: 0.7852 (m-30) cc_final: 0.7242 (m-30) REVERT: I 27 LYS cc_start: 0.7284 (ptpt) cc_final: 0.6957 (ptpp) REVERT: I 51 SER cc_start: 0.7823 (t) cc_final: 0.7546 (p) REVERT: I 67 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8371 (mp10) REVERT: I 93 GLU cc_start: 0.8282 (tt0) cc_final: 0.7925 (tt0) REVERT: K 110 LYS cc_start: 0.8255 (ttmm) cc_final: 0.8018 (mtpp) REVERT: L 42 ARG cc_start: 0.8221 (mtt-85) cc_final: 0.8000 (mtp85) REVERT: R 76 MET cc_start: 0.5588 (mmm) cc_final: 0.5072 (mmm) REVERT: R 104 LEU cc_start: 0.8558 (mm) cc_final: 0.8133 (pp) REVERT: R 170 LEU cc_start: 0.1272 (mt) cc_final: 0.0891 (tm) REVERT: R 185 CYS cc_start: 0.4988 (OUTLIER) cc_final: 0.3637 (t) REVERT: R 189 ILE cc_start: 0.4039 (OUTLIER) cc_final: 0.2633 (mt) REVERT: D 33 LEU cc_start: 0.2070 (OUTLIER) cc_final: 0.1690 (mm) REVERT: D 62 MET cc_start: 0.3488 (mmp) cc_final: 0.3010 (mmp) REVERT: G 1 MET cc_start: 0.5277 (OUTLIER) cc_final: 0.3936 (ppp) outliers start: 140 outliers final: 81 residues processed: 493 average time/residue: 1.4865 time to fit residues: 852.0007 Evaluate side-chains 487 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 384 time to evaluate : 3.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 552 ASP Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 849 ASP Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain F residue 51 ARG Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 43 ASP Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 122 ARG Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 119 ILE Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 131 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 319 optimal weight: 0.0770 chunk 37 optimal weight: 4.9990 chunk 188 optimal weight: 0.5980 chunk 241 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 chunk 329 optimal weight: 5.9990 chunk 206 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN B 582 GLN ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN H 44 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28484 Z= 0.187 Angle : 0.590 13.583 38477 Z= 0.296 Chirality : 0.045 0.241 4304 Planarity : 0.004 0.058 4983 Dihedral : 5.207 58.273 3815 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.35 % Favored : 94.62 % Rotamer: Outliers : 4.34 % Allowed : 19.99 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: -0.81 (0.14), residues: 3441 helix: 0.52 (0.15), residues: 1208 sheet: -1.09 (0.23), residues: 493 loop : -1.09 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 679 HIS 0.006 0.001 HIS R 177 PHE 0.025 0.001 PHE B 422 TYR 0.022 0.001 TYR E 182 ARG 0.012 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 397 time to evaluate : 3.401 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 502 ASN cc_start: 0.8266 (p0) cc_final: 0.8017 (p0) REVERT: A 504 HIS cc_start: 0.7389 (t-90) cc_final: 0.6311 (m90) REVERT: A 508 SER cc_start: 0.8103 (OUTLIER) cc_final: 0.7863 (p) REVERT: A 509 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6999 (tt) REVERT: A 711 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6998 (mt0) REVERT: A 769 MET cc_start: 0.7211 (mtt) cc_final: 0.6960 (mtt) REVERT: A 803 LYS cc_start: 0.7782 (tppp) cc_final: 0.7362 (ttpp) REVERT: A 859 TYR cc_start: 0.7807 (t80) cc_final: 0.7508 (t80) REVERT: A 866 LYS cc_start: 0.7863 (tmmt) cc_final: 0.7535 (pptt) REVERT: A 927 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: A 947 HIS cc_start: 0.6783 (t70) cc_final: 0.6530 (t-170) REVERT: A 951 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6766 (mt-10) REVERT: A 1015 GLU cc_start: 0.6932 (mp0) cc_final: 0.6633 (mp0) REVERT: A 1102 MET cc_start: 0.6447 (mtm) cc_final: 0.6195 (mtm) REVERT: A 1230 GLN cc_start: 0.8991 (mt0) cc_final: 0.8718 (mt0) REVERT: A 1233 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7994 (mm-30) REVERT: A 1271 GLU cc_start: 0.2183 (OUTLIER) cc_final: 0.1520 (mp0) REVERT: A 1279 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7267 (ptp) REVERT: A 1293 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7403 (tt) REVERT: A 1310 HIS cc_start: 0.7527 (p90) cc_final: 0.7237 (p90) REVERT: A 1339 ASP cc_start: 0.7910 (t0) cc_final: 0.7336 (m-30) REVERT: A 1355 VAL cc_start: 0.8449 (m) cc_final: 0.8150 (t) REVERT: A 1412 MET cc_start: 0.6357 (mmm) cc_final: 0.6122 (mmm) REVERT: B 92 TYR cc_start: 0.7382 (m-80) cc_final: 0.6807 (m-80) REVERT: B 155 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8519 (ttm) REVERT: B 160 TYR cc_start: 0.7761 (m-80) cc_final: 0.7427 (m-80) REVERT: B 169 ARG cc_start: 0.7311 (mtp-110) cc_final: 0.6942 (ttt-90) REVERT: B 170 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7622 (m-30) REVERT: B 309 PHE cc_start: 0.8846 (t80) cc_final: 0.8606 (t80) REVERT: B 334 LYS cc_start: 0.7737 (tppp) cc_final: 0.7172 (ttpp) REVERT: B 433 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7521 (pt) REVERT: B 452 ASN cc_start: 0.8491 (m-40) cc_final: 0.8264 (m-40) REVERT: B 508 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.7658 (mtt) REVERT: B 764 MET cc_start: 0.8574 (mtm) cc_final: 0.8314 (mtm) REVERT: B 817 GLN cc_start: 0.8393 (pt0) cc_final: 0.8155 (pt0) REVERT: B 913 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7800 (mt0) REVERT: B 941 GLN cc_start: 0.5924 (tp40) cc_final: 0.5709 (tp40) REVERT: B 965 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8510 (mm) REVERT: C 5 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.7954 (p0) REVERT: C 126 ARG cc_start: 0.7377 (mtm180) cc_final: 0.7023 (ptm160) REVERT: C 260 GLN cc_start: 0.8237 (tp-100) cc_final: 0.7732 (tt0) REVERT: C 262 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7403 (mp10) REVERT: E 79 GLU cc_start: 0.8756 (mp0) cc_final: 0.8160 (pm20) REVERT: F 62 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6952 (mtp-110) REVERT: H 51 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7616 (p0) REVERT: H 54 ASP cc_start: 0.7850 (m-30) cc_final: 0.7207 (m-30) REVERT: H 92 MET cc_start: 0.8812 (mtt) cc_final: 0.8386 (mtt) REVERT: I 51 SER cc_start: 0.7755 (t) cc_final: 0.7459 (p) REVERT: I 93 GLU cc_start: 0.8276 (tt0) cc_final: 0.7934 (tt0) REVERT: K 110 LYS cc_start: 0.8279 (ttmm) cc_final: 0.8033 (mtpp) REVERT: L 21 GLU cc_start: 0.8121 (tt0) cc_final: 0.7908 (pt0) REVERT: L 42 ARG cc_start: 0.8227 (mtt-85) cc_final: 0.8009 (mtp85) REVERT: R 76 MET cc_start: 0.5628 (mmm) cc_final: 0.5080 (mmm) REVERT: R 104 LEU cc_start: 0.8610 (mm) cc_final: 0.8185 (pp) REVERT: R 170 LEU cc_start: 0.1238 (mt) cc_final: 0.0947 (tm) REVERT: R 185 CYS cc_start: 0.5194 (OUTLIER) cc_final: 0.3941 (t) REVERT: R 189 ILE cc_start: 0.4004 (OUTLIER) cc_final: 0.2728 (mt) REVERT: G 1 MET cc_start: 0.5548 (OUTLIER) cc_final: 0.4147 (ppp) outliers start: 134 outliers final: 68 residues processed: 485 average time/residue: 1.4452 time to fit residues: 812.8401 Evaluate side-chains 475 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 387 time to evaluate : 3.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 552 ASP Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1160 ARG Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 849 ASP Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 43 ASP Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 122 ARG Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 119 ILE Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 203 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 224 optimal weight: 7.9990 chunk 162 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 259 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A1384 HIS A1410 HIS B 265 GLN B 582 GLN ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN E 174 GLN H 44 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 28484 Z= 0.288 Angle : 0.618 13.112 38477 Z= 0.310 Chirality : 0.046 0.255 4304 Planarity : 0.004 0.059 4983 Dihedral : 5.201 59.006 3815 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.73 % Favored : 94.25 % Rotamer: Outliers : 4.34 % Allowed : 20.25 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: -0.72 (0.14), residues: 3441 helix: 0.59 (0.15), residues: 1210 sheet: -1.04 (0.23), residues: 494 loop : -1.04 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 27 HIS 0.014 0.001 HIS R 60 PHE 0.022 0.002 PHE A 592 TYR 0.022 0.001 TYR E 182 ARG 0.012 0.000 ARG B 770 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 394 time to evaluate : 3.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 ASN cc_start: 0.8262 (p0) cc_final: 0.8033 (p0) REVERT: A 504 HIS cc_start: 0.7418 (t-90) cc_final: 0.6270 (m90) REVERT: A 508 SER cc_start: 0.8137 (OUTLIER) cc_final: 0.7863 (p) REVERT: A 509 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.7024 (tt) REVERT: A 711 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.7008 (mt0) REVERT: A 769 MET cc_start: 0.7200 (mtt) cc_final: 0.6945 (mtt) REVERT: A 803 LYS cc_start: 0.7810 (tppp) cc_final: 0.7379 (ttpp) REVERT: A 859 TYR cc_start: 0.7757 (t80) cc_final: 0.7487 (t80) REVERT: A 927 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7255 (tm-30) REVERT: A 947 HIS cc_start: 0.6840 (t70) cc_final: 0.6580 (t-170) REVERT: A 951 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6755 (mt-10) REVERT: A 1015 GLU cc_start: 0.6966 (mp0) cc_final: 0.6670 (mp0) REVERT: A 1230 GLN cc_start: 0.8987 (mt0) cc_final: 0.8708 (mt0) REVERT: A 1233 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7986 (mm-30) REVERT: A 1279 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7633 (mtm) REVERT: A 1293 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7409 (tt) REVERT: A 1310 HIS cc_start: 0.7526 (p90) cc_final: 0.7237 (p90) REVERT: A 1339 ASP cc_start: 0.7945 (t0) cc_final: 0.7386 (m-30) REVERT: B 51 ILE cc_start: 0.8932 (tp) cc_final: 0.8646 (tp) REVERT: B 92 TYR cc_start: 0.7356 (m-80) cc_final: 0.6769 (m-80) REVERT: B 155 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8552 (ttm) REVERT: B 169 ARG cc_start: 0.7250 (mtp-110) cc_final: 0.6895 (ttt-90) REVERT: B 170 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7612 (m-30) REVERT: B 309 PHE cc_start: 0.8844 (t80) cc_final: 0.8612 (t80) REVERT: B 334 LYS cc_start: 0.7748 (tppp) cc_final: 0.7235 (ttpp) REVERT: B 407 MET cc_start: 0.7439 (mtt) cc_final: 0.7176 (mtt) REVERT: B 433 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7458 (pt) REVERT: B 452 ASN cc_start: 0.8543 (m-40) cc_final: 0.8279 (m-40) REVERT: B 508 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.7756 (mtt) REVERT: B 764 MET cc_start: 0.8609 (mtm) cc_final: 0.8380 (mtm) REVERT: B 913 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7775 (mt0) REVERT: B 965 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8630 (mm) REVERT: C 5 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.7945 (p0) REVERT: C 126 ARG cc_start: 0.7350 (mtm180) cc_final: 0.7036 (ptm160) REVERT: C 262 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7424 (mp10) REVERT: E 79 GLU cc_start: 0.8775 (mp0) cc_final: 0.8165 (pm20) REVERT: F 51 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6232 (mtp180) REVERT: F 62 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7096 (mtp-110) REVERT: H 54 ASP cc_start: 0.7836 (m-30) cc_final: 0.7473 (m-30) REVERT: H 92 MET cc_start: 0.8853 (mtt) cc_final: 0.8460 (mtt) REVERT: I 51 SER cc_start: 0.7710 (t) cc_final: 0.7440 (p) REVERT: I 93 GLU cc_start: 0.8291 (tt0) cc_final: 0.7943 (tt0) REVERT: K 110 LYS cc_start: 0.8290 (ttmm) cc_final: 0.8043 (mtpp) REVERT: L 21 GLU cc_start: 0.8142 (tt0) cc_final: 0.7882 (pt0) REVERT: L 42 ARG cc_start: 0.8221 (mtt-85) cc_final: 0.7837 (mtp85) REVERT: R 55 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7299 (pm20) REVERT: R 76 MET cc_start: 0.5671 (mmm) cc_final: 0.5122 (mmm) REVERT: R 104 LEU cc_start: 0.8608 (mm) cc_final: 0.8211 (pp) REVERT: R 170 LEU cc_start: 0.1197 (mt) cc_final: 0.0862 (tm) REVERT: R 185 CYS cc_start: 0.4912 (OUTLIER) cc_final: 0.3916 (t) REVERT: R 189 ILE cc_start: 0.3872 (OUTLIER) cc_final: 0.2644 (mt) REVERT: D 33 LEU cc_start: 0.1907 (OUTLIER) cc_final: 0.1533 (mm) REVERT: D 62 MET cc_start: 0.3402 (mmp) cc_final: 0.2930 (mmp) REVERT: G 1 MET cc_start: 0.5476 (OUTLIER) cc_final: 0.4003 (ppp) REVERT: G 164 MET cc_start: 0.1242 (mmt) cc_final: -0.0011 (pp-130) outliers start: 134 outliers final: 82 residues processed: 482 average time/residue: 1.4882 time to fit residues: 833.0462 Evaluate side-chains 481 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 378 time to evaluate : 3.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 552 ASP Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1086 MET Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 849 ASP Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain F residue 51 ARG Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 43 ASP Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 122 ARG Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 119 ILE Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 200 PHE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 299 optimal weight: 0.9980 chunk 315 optimal weight: 20.0000 chunk 288 optimal weight: 0.8980 chunk 307 optimal weight: 9.9990 chunk 184 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 277 optimal weight: 0.9980 chunk 290 optimal weight: 0.0970 chunk 306 optimal weight: 3.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 GLN A 671 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS B 265 GLN B 582 GLN ** B 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 HIS ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN H 44 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28484 Z= 0.203 Angle : 0.599 14.608 38477 Z= 0.299 Chirality : 0.045 0.287 4304 Planarity : 0.004 0.061 4983 Dihedral : 5.058 55.196 3815 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.35 % Favored : 94.62 % Rotamer: Outliers : 4.08 % Allowed : 20.67 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: -0.58 (0.15), residues: 3441 helix: 0.75 (0.15), residues: 1215 sheet: -0.95 (0.23), residues: 492 loop : -1.01 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 679 HIS 0.007 0.001 HIS R 177 PHE 0.020 0.001 PHE A 592 TYR 0.024 0.001 TYR E 182 ARG 0.013 0.000 ARG B 770 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 391 time to evaluate : 3.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 HIS cc_start: 0.7403 (t-90) cc_final: 0.6308 (m90) REVERT: A 508 SER cc_start: 0.7944 (OUTLIER) cc_final: 0.7719 (p) REVERT: A 509 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6961 (tt) REVERT: A 711 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.7015 (mt0) REVERT: A 803 LYS cc_start: 0.7793 (tppp) cc_final: 0.7345 (ttpp) REVERT: A 859 TYR cc_start: 0.7796 (t80) cc_final: 0.7512 (t80) REVERT: A 927 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7203 (tm-30) REVERT: A 947 HIS cc_start: 0.6764 (t70) cc_final: 0.6505 (t-170) REVERT: A 951 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6759 (mt-10) REVERT: A 954 ARG cc_start: 0.7077 (mtt-85) cc_final: 0.6788 (mtt-85) REVERT: A 1015 GLU cc_start: 0.6949 (mp0) cc_final: 0.6638 (mp0) REVERT: A 1102 MET cc_start: 0.6244 (OUTLIER) cc_final: 0.5978 (mtm) REVERT: A 1230 GLN cc_start: 0.8970 (mt0) cc_final: 0.8670 (mt0) REVERT: A 1233 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7984 (mm-30) REVERT: A 1271 GLU cc_start: 0.2564 (OUTLIER) cc_final: 0.1920 (mp0) REVERT: A 1279 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7315 (ptp) REVERT: A 1293 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7379 (tt) REVERT: A 1310 HIS cc_start: 0.7492 (p90) cc_final: 0.7206 (p90) REVERT: A 1339 ASP cc_start: 0.7857 (t0) cc_final: 0.7353 (m-30) REVERT: A 1355 VAL cc_start: 0.8416 (m) cc_final: 0.8084 (t) REVERT: B 51 ILE cc_start: 0.8951 (tp) cc_final: 0.8683 (tp) REVERT: B 92 TYR cc_start: 0.7367 (m-80) cc_final: 0.6757 (m-80) REVERT: B 155 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8524 (ttm) REVERT: B 160 TYR cc_start: 0.7712 (m-80) cc_final: 0.7387 (m-80) REVERT: B 169 ARG cc_start: 0.7285 (mtp-110) cc_final: 0.6926 (ttt-90) REVERT: B 170 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7538 (m-30) REVERT: B 309 PHE cc_start: 0.8839 (t80) cc_final: 0.8627 (t80) REVERT: B 334 LYS cc_start: 0.7750 (tppp) cc_final: 0.7182 (ttpp) REVERT: B 407 MET cc_start: 0.7344 (mtt) cc_final: 0.7084 (mtt) REVERT: B 433 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7429 (pt) REVERT: B 452 ASN cc_start: 0.8583 (m-40) cc_final: 0.8292 (m-40) REVERT: B 508 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.7726 (mtt) REVERT: B 764 MET cc_start: 0.8561 (mtm) cc_final: 0.8291 (mtm) REVERT: B 770 ARG cc_start: 0.7502 (mtm110) cc_final: 0.7018 (ttp80) REVERT: B 817 GLN cc_start: 0.8309 (pt0) cc_final: 0.8096 (pt0) REVERT: B 913 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7822 (mt0) REVERT: B 965 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8494 (mm) REVERT: C 5 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.7930 (p0) REVERT: C 126 ARG cc_start: 0.7410 (mtm180) cc_final: 0.7056 (ptm160) REVERT: C 262 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7371 (mp10) REVERT: E 79 GLU cc_start: 0.8791 (mp0) cc_final: 0.8189 (pm20) REVERT: E 129 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8460 (tm-30) REVERT: F 62 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7105 (mtp-110) REVERT: F 117 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7333 (t0) REVERT: H 35 PHE cc_start: 0.8225 (m-10) cc_final: 0.7878 (m-80) REVERT: H 54 ASP cc_start: 0.7834 (m-30) cc_final: 0.7476 (m-30) REVERT: I 51 SER cc_start: 0.7689 (t) cc_final: 0.7401 (p) REVERT: I 93 GLU cc_start: 0.8280 (tt0) cc_final: 0.7909 (tt0) REVERT: J 48 MET cc_start: 0.9122 (mmm) cc_final: 0.8894 (mmm) REVERT: K 96 SER cc_start: 0.8578 (OUTLIER) cc_final: 0.8357 (p) REVERT: K 110 LYS cc_start: 0.8245 (ttmm) cc_final: 0.7670 (mptt) REVERT: L 42 ARG cc_start: 0.8221 (mtt-85) cc_final: 0.7852 (mtp85) REVERT: R 76 MET cc_start: 0.5694 (mmm) cc_final: 0.5061 (mmm) REVERT: R 104 LEU cc_start: 0.8550 (mm) cc_final: 0.8171 (pp) REVERT: R 170 LEU cc_start: 0.1606 (mt) cc_final: 0.1280 (tm) REVERT: R 185 CYS cc_start: 0.4472 (OUTLIER) cc_final: 0.3574 (t) REVERT: R 189 ILE cc_start: 0.3663 (OUTLIER) cc_final: 0.2586 (mt) REVERT: D 33 LEU cc_start: 0.2117 (OUTLIER) cc_final: 0.1577 (pt) REVERT: G 1 MET cc_start: 0.5497 (OUTLIER) cc_final: 0.4027 (ppp) REVERT: G 117 MET cc_start: -0.2164 (mtt) cc_final: -0.3004 (pp-130) outliers start: 126 outliers final: 72 residues processed: 474 average time/residue: 1.4682 time to fit residues: 805.8353 Evaluate side-chains 470 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 374 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 552 ASP Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1160 ARG Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 849 ASP Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 43 ASP Chi-restraints excluded: chain I residue 122 ARG Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 119 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 200 PHE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 201 optimal weight: 1.9990 chunk 324 optimal weight: 6.9990 chunk 198 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 340 optimal weight: 7.9990 chunk 313 optimal weight: 20.0000 chunk 271 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 166 optimal weight: 0.0980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN A 671 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS B 265 GLN B 582 GLN ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN E 132 GLN H 44 ASN I 18 GLN L 26 ASN G 14 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 28484 Z= 0.265 Angle : 0.624 18.059 38477 Z= 0.310 Chirality : 0.046 0.247 4304 Planarity : 0.004 0.062 4983 Dihedral : 5.058 53.229 3815 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.78 % Favored : 94.19 % Rotamer: Outliers : 3.76 % Allowed : 21.22 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: -0.55 (0.15), residues: 3441 helix: 0.75 (0.15), residues: 1214 sheet: -0.91 (0.23), residues: 492 loop : -0.96 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 27 HIS 0.018 0.001 HIS R 60 PHE 0.022 0.001 PHE A 592 TYR 0.024 0.001 TYR E 182 ARG 0.013 0.001 ARG B 770 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 379 time to evaluate : 3.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 HIS cc_start: 0.7396 (t-90) cc_final: 0.6235 (m90) REVERT: A 508 SER cc_start: 0.7947 (m) cc_final: 0.7710 (p) REVERT: A 509 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6972 (tt) REVERT: A 711 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.7022 (mt0) REVERT: A 803 LYS cc_start: 0.7824 (tppp) cc_final: 0.7367 (ttpp) REVERT: A 859 TYR cc_start: 0.7800 (t80) cc_final: 0.7521 (t80) REVERT: A 902 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7784 (pt0) REVERT: A 927 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: A 947 HIS cc_start: 0.6783 (t70) cc_final: 0.6530 (t-170) REVERT: A 951 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6762 (mt-10) REVERT: A 954 ARG cc_start: 0.7092 (mtt-85) cc_final: 0.6854 (mtt-85) REVERT: A 1015 GLU cc_start: 0.6997 (mp0) cc_final: 0.6546 (mp0) REVERT: A 1102 MET cc_start: 0.6333 (OUTLIER) cc_final: 0.6053 (mtm) REVERT: A 1230 GLN cc_start: 0.8966 (mt0) cc_final: 0.8663 (mt0) REVERT: A 1233 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7991 (mm-30) REVERT: A 1269 MET cc_start: 0.1198 (pmm) cc_final: 0.0711 (mmt) REVERT: A 1271 GLU cc_start: 0.2470 (OUTLIER) cc_final: 0.1773 (mp0) REVERT: A 1279 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7297 (ptp) REVERT: A 1293 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7333 (tt) REVERT: A 1310 HIS cc_start: 0.7515 (p90) cc_final: 0.7219 (p90) REVERT: A 1339 ASP cc_start: 0.7909 (t0) cc_final: 0.7397 (m-30) REVERT: A 1355 VAL cc_start: 0.8366 (m) cc_final: 0.8081 (t) REVERT: B 51 ILE cc_start: 0.8939 (tp) cc_final: 0.8679 (tp) REVERT: B 92 TYR cc_start: 0.7342 (m-80) cc_final: 0.6760 (m-80) REVERT: B 155 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8553 (ttm) REVERT: B 160 TYR cc_start: 0.7742 (m-80) cc_final: 0.7398 (m-80) REVERT: B 169 ARG cc_start: 0.7367 (mtp-110) cc_final: 0.7011 (ttt-90) REVERT: B 170 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7555 (m-30) REVERT: B 309 PHE cc_start: 0.8826 (t80) cc_final: 0.8621 (t80) REVERT: B 334 LYS cc_start: 0.7764 (tppp) cc_final: 0.7219 (ttpp) REVERT: B 433 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7352 (pt) REVERT: B 452 ASN cc_start: 0.8589 (m-40) cc_final: 0.8311 (m-40) REVERT: B 508 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.7751 (mtt) REVERT: B 744 MET cc_start: 0.9246 (mtt) cc_final: 0.8729 (mmt) REVERT: B 764 MET cc_start: 0.8592 (mtm) cc_final: 0.8362 (mtm) REVERT: B 770 ARG cc_start: 0.7554 (mtm110) cc_final: 0.7073 (ttp80) REVERT: B 817 GLN cc_start: 0.8375 (pt0) cc_final: 0.8163 (pt0) REVERT: B 965 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8606 (mm) REVERT: C 5 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.7896 (p0) REVERT: C 126 ARG cc_start: 0.7349 (mtm180) cc_final: 0.7052 (ptm160) REVERT: C 262 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7401 (mp10) REVERT: E 79 GLU cc_start: 0.8786 (mp0) cc_final: 0.8193 (pm20) REVERT: F 62 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7127 (mtp-110) REVERT: F 117 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7411 (t0) REVERT: H 35 PHE cc_start: 0.8223 (m-10) cc_final: 0.7864 (m-80) REVERT: H 54 ASP cc_start: 0.7882 (m-30) cc_final: 0.7507 (m-30) REVERT: H 92 MET cc_start: 0.8838 (mtt) cc_final: 0.8434 (mtt) REVERT: I 51 SER cc_start: 0.7671 (t) cc_final: 0.7393 (p) REVERT: I 93 GLU cc_start: 0.8278 (tt0) cc_final: 0.7913 (tt0) REVERT: J 48 MET cc_start: 0.9143 (mmm) cc_final: 0.8794 (mmm) REVERT: K 96 SER cc_start: 0.8614 (OUTLIER) cc_final: 0.8400 (p) REVERT: K 110 LYS cc_start: 0.8276 (ttmm) cc_final: 0.7669 (mptt) REVERT: L 42 ARG cc_start: 0.8197 (mtt-85) cc_final: 0.7833 (mtp85) REVERT: R 55 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7382 (pm20) REVERT: R 76 MET cc_start: 0.5680 (mmm) cc_final: 0.5199 (mmm) REVERT: R 104 LEU cc_start: 0.8543 (mm) cc_final: 0.8168 (pp) REVERT: R 170 LEU cc_start: 0.1665 (mt) cc_final: 0.1297 (tm) REVERT: R 185 CYS cc_start: 0.4015 (OUTLIER) cc_final: 0.3312 (t) REVERT: R 189 ILE cc_start: 0.3517 (OUTLIER) cc_final: 0.2563 (mt) REVERT: D 33 LEU cc_start: 0.2104 (OUTLIER) cc_final: 0.1611 (pt) REVERT: D 62 MET cc_start: 0.3211 (mmp) cc_final: 0.2712 (mmp) REVERT: G 1 MET cc_start: 0.5526 (OUTLIER) cc_final: 0.4039 (ppp) REVERT: G 99 THR cc_start: 0.0758 (OUTLIER) cc_final: 0.0555 (t) REVERT: G 117 MET cc_start: -0.2166 (mtt) cc_final: -0.2999 (pp-130) outliers start: 116 outliers final: 75 residues processed: 460 average time/residue: 1.4797 time to fit residues: 791.9807 Evaluate side-chains 473 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 374 time to evaluate : 3.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 552 ASP Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1362 ILE Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 849 ASP Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 43 ASP Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 122 ARG Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 119 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 200 PHE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 215 optimal weight: 0.2980 chunk 289 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 250 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 271 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 279 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN A 671 ASN A1384 HIS B 265 GLN B 582 GLN ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN E 108 GLN E 129 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN I 18 GLN L 26 ASN G 14 HIS G 21 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.181746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115739 restraints weight = 32205.631| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.34 r_work: 0.3426 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28484 Z= 0.196 Angle : 0.600 13.456 38477 Z= 0.298 Chirality : 0.045 0.239 4304 Planarity : 0.004 0.057 4983 Dihedral : 4.932 54.685 3815 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.17 % Favored : 94.80 % Rotamer: Outliers : 3.50 % Allowed : 21.54 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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 (0.15), residues: 3441 helix: 0.90 (0.15), residues: 1210 sheet: -0.83 (0.23), residues: 488 loop : -0.92 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 27 HIS 0.021 0.001 HIS R 60 PHE 0.019 0.001 PHE A 592 TYR 0.025 0.001 TYR E 182 ARG 0.016 0.001 ARG A1408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12950.08 seconds wall clock time: 229 minutes 31.52 seconds (13771.52 seconds total)