Starting phenix.real_space_refine on Sun Feb 18 01:11:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8g_16475/02_2024/8c8g_16475.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8g_16475/02_2024/8c8g_16475.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8g_16475/02_2024/8c8g_16475.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8g_16475/02_2024/8c8g_16475.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8g_16475/02_2024/8c8g_16475.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8g_16475/02_2024/8c8g_16475.pdb" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.040 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: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 12995 2.51 5 N 3303 2.21 5 O 4013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 5": "OE1" <-> "OE2" Residue "A ARG 35": "NH1" <-> "NH2" Residue "A ARG 127": "NH1" <-> "NH2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A ARG 472": "NH1" <-> "NH2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A GLU 635": "OE1" <-> "OE2" Residue "A GLU 645": "OE1" <-> "OE2" Residue "A GLU 718": "OE1" <-> "OE2" Residue "A GLU 837": "OE1" <-> "OE2" Residue "A TYR 992": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 999": "NH1" <-> "NH2" Residue "A GLU 1007": "OE1" <-> "OE2" Residue "A ARG 1054": "NH1" <-> "NH2" Residue "A TYR 1108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1123": "NH1" <-> "NH2" Residue "A GLU 1131": "OE1" <-> "OE2" Residue "A ARG 1301": "NH1" <-> "NH2" Residue "B ARG 40": "NH1" <-> "NH2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B GLU 351": "OE1" <-> "OE2" Residue "B GLU 358": "OE1" <-> "OE2" Residue "B GLU 592": "OE1" <-> "OE2" Residue "B PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 787": "OE1" <-> "OE2" Residue "B GLU 919": "OE1" <-> "OE2" Residue "B ARG 1003": "NH1" <-> "NH2" Residue "B ARG 1010": "NH1" <-> "NH2" Residue "B ARG 1084": "NH1" <-> "NH2" Residue "B GLU 1139": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20362 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10790 Classifications: {'peptide': 1335} Link IDs: {'PTRANS': 37, 'TRANS': 1297} Chain: "B" Number of atoms: 9572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1195, 9572 Classifications: {'peptide': 1195} Link IDs: {'PTRANS': 39, 'TRANS': 1155} Time building chain proxies: 10.50, per 1000 atoms: 0.52 Number of scatterers: 20362 At special positions: 0 Unit cell: (127.92, 116.44, 151.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 4013 8.00 N 3303 7.00 C 12995 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 366 " distance=2.07 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: 7.44 Conformation dependent library (CDL) restraints added in 3.6 seconds 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4806 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 36 sheets defined 26.3% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 25 through 29 Processing helix chain 'A' and resid 100 through 122 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.813A pdb=" N PHE A 132 " --> pdb=" O TYR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 261 removed outlier: 3.907A pdb=" N LEU A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 294 through 300 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 331 through 335 removed outlier: 3.590A pdb=" N SER A 335 " --> pdb=" O PRO A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 356 through 367 Processing helix chain 'A' and resid 373 through 376 removed outlier: 3.975A pdb=" N LYS A 376 " --> pdb=" O GLN A 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 373 through 376' Processing helix chain 'A' and resid 385 through 391 Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 396 through 404 Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.531A pdb=" N THR A 413 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 414 " --> pdb=" O TYR A 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 414' Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 591 through 596 removed outlier: 3.656A pdb=" N PHE A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.574A pdb=" N GLU A 615 " --> pdb=" O MET A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 639 Processing helix chain 'A' and resid 659 through 666 Processing helix chain 'A' and resid 671 through 676 Processing helix chain 'A' and resid 716 through 750 removed outlier: 4.019A pdb=" N VAL A 728 " --> pdb=" O PHE A 724 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 740 " --> pdb=" O LYS A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 781 removed outlier: 3.525A pdb=" N THR A 774 " --> pdb=" O LYS A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 801 Processing helix chain 'A' and resid 803 through 830 Processing helix chain 'A' and resid 830 through 861 removed outlier: 3.565A pdb=" N GLN A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLU A 855 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 856 " --> pdb=" O ASP A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 879 Processing helix chain 'A' and resid 883 through 905 removed outlier: 3.510A pdb=" N VAL A 896 " --> pdb=" O ALA A 892 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 897 " --> pdb=" O HIS A 893 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 902 " --> pdb=" O LYS A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1133 removed outlier: 3.865A pdb=" N HIS A1133 " --> pdb=" O PHE A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1290 Processing helix chain 'B' and resid 69 through 88 removed outlier: 3.537A pdb=" N LEU B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 101 Processing helix chain 'B' and resid 152 through 156 removed outlier: 3.530A pdb=" N SER B 155 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 removed outlier: 3.531A pdb=" N GLY B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE B 196 " --> pdb=" O THR B 192 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG B 197 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 229 Processing helix chain 'B' and resid 248 through 260 removed outlier: 3.569A pdb=" N ALA B 259 " --> pdb=" O LYS B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 280 removed outlier: 3.647A pdb=" N TYR B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 289 Processing helix chain 'B' and resid 309 through 315 Processing helix chain 'B' and resid 391 through 397 removed outlier: 3.642A pdb=" N THR B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 442 removed outlier: 3.558A pdb=" N ALA B 440 " --> pdb=" O LEU B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 450 removed outlier: 3.815A pdb=" N ILE B 450 " --> pdb=" O LEU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 463 removed outlier: 4.522A pdb=" N ASP B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 479 Processing helix chain 'B' and resid 484 through 500 removed outlier: 4.075A pdb=" N PHE B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU B 494 " --> pdb=" O GLY B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 528 Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 559 through 561 No H-bonds generated for 'chain 'B' and resid 559 through 561' Processing helix chain 'B' and resid 562 through 575 removed outlier: 4.264A pdb=" N TYR B 566 " --> pdb=" O GLN B 562 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE B 568 " --> pdb=" O LYS B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 603 removed outlier: 3.809A pdb=" N LEU B 582 " --> pdb=" O ARG B 578 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 585 " --> pdb=" O ARG B 581 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 603 " --> pdb=" O SER B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 650 removed outlier: 3.531A pdb=" N TYR B 626 " --> pdb=" O TYR B 622 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 632 " --> pdb=" O LEU B 628 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 633 " --> pdb=" O SER B 629 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 645 " --> pdb=" O LYS B 641 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 648 " --> pdb=" O VAL B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 662 Processing helix chain 'B' and resid 665 through 674 removed outlier: 3.653A pdb=" N LEU B 671 " --> pdb=" O ASP B 667 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 41 removed outlier: 6.896A pdb=" N ILE A 63 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL A 186 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 167 removed outlier: 3.926A pdb=" N GLY A 179 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU A 166 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LYS A 177 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 239 through 241 removed outlier: 3.511A pdb=" N THR A 451 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 277 through 282 Processing sheet with id=AA7, first strand: chain 'A' and resid 370 through 371 removed outlier: 3.520A pdb=" N LYS A 370 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 474 through 477 removed outlier: 7.734A pdb=" N VAL A 560 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLU A 464 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 562 " --> pdb=" O GLU A 464 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLU A 466 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 589 Processing sheet with id=AB1, first strand: chain 'A' and resid 644 through 645 Processing sheet with id=AB2, first strand: chain 'A' and resid 923 through 924 Processing sheet with id=AB3, first strand: chain 'A' and resid 941 through 944 removed outlier: 3.967A pdb=" N VAL A 976 " --> pdb=" O PHE A1099 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE A1011 " --> pdb=" O TYR A1102 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU A1029 " --> pdb=" O ILE A1011 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER A1013 " --> pdb=" O LEU A1027 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU A1027 " --> pdb=" O SER A1013 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N SER A1015 " --> pdb=" O GLU A1025 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLU A1025 " --> pdb=" O SER A1015 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A1017 " --> pdb=" O GLU A1023 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU A1023 " --> pdb=" O VAL A1017 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A1036 " --> pdb=" O ILE A1051 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 952 through 953 removed outlier: 10.918A pdb=" N GLN A 958 " --> pdb=" O ASP A1112 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ASP A1112 " --> pdb=" O GLN A 958 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LEU A1110 " --> pdb=" O ARG A 999 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ARG A 999 " --> pdb=" O LEU A1110 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ASP A1112 " --> pdb=" O TRP A 997 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TRP A 997 " --> pdb=" O ASP A1112 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A1072 " --> pdb=" O LEU A1083 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU A1083 " --> pdb=" O ILE A1072 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A1074 " --> pdb=" O LEU A1081 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1220 through 1223 Processing sheet with id=AB6, first strand: chain 'A' and resid 1160 through 1161 Processing sheet with id=AB7, first strand: chain 'A' and resid 1179 through 1180 Processing sheet with id=AB8, first strand: chain 'A' and resid 1229 through 1235 Processing sheet with id=AB9, first strand: chain 'A' and resid 1259 through 1261 removed outlier: 5.194A pdb=" N LEU A1273 " --> pdb=" O ILE A1297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1278 through 1279 Processing sheet with id=AC2, first strand: chain 'B' and resid 125 through 130 removed outlier: 3.991A pdb=" N HIS B 127 " --> pdb=" O CYS B 118 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN B 117 " --> pdb=" O ARG B 11 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN B 9 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU B 23 " --> pdb=" O TYR B 12 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL B 34 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TRP B 35 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL B 134 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 179 through 181 removed outlier: 3.569A pdb=" N ARG B 179 " --> pdb=" O ASN B 174 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE B 172 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 207 through 212 removed outlier: 6.539A pdb=" N TYR B 219 " --> pdb=" O PHE B 210 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 340 through 341 removed outlier: 6.263A pdb=" N LYS B 340 " --> pdb=" O THR B 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC7, first strand: chain 'B' and resid 502 through 503 Processing sheet with id=AC8, first strand: chain 'B' and resid 690 through 694 removed outlier: 7.638A pdb=" N SER B 711 " --> pdb=" O PRO B 700 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU B 702 " --> pdb=" O ILE B 709 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP B 707 " --> pdb=" O LEU B 704 " (cutoff:3.500A) removed outlier: 9.774A pdb=" N GLU B 708 " --> pdb=" O ASN B 739 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASN B 739 " --> pdb=" O GLU B 708 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE B 736 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 715 through 718 removed outlier: 6.592A pdb=" N LEU B 850 " --> pdb=" O LYS B 756 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS B 756 " --> pdb=" O LEU B 850 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 852 " --> pdb=" O THR B 754 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ASP B 815 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU B 821 " --> pdb=" O ASP B 815 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 943 through 947 removed outlier: 7.989A pdb=" N LEU B 928 " --> pdb=" O GLU B 888 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU B 888 " --> pdb=" O LEU B 928 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 902 through 905 removed outlier: 4.381A pdb=" N LEU B1011 " --> pdb=" O PRO B 912 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 955 through 959 removed outlier: 3.523A pdb=" N TYR B 955 " --> pdb=" O VAL B 966 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 988 through 992 Processing sheet with id=AD5, first strand: chain 'B' and resid 1047 through 1050 Processing sheet with id=AD6, first strand: chain 'B' and resid 1055 through 1056 removed outlier: 6.515A pdb=" N LEU B1055 " --> pdb=" O LYS B1121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 1085 through 1088 Processing sheet with id=AD8, first strand: chain 'B' and resid 1126 through 1128 removed outlier: 3.979A pdb=" N SER B1126 " --> pdb=" O ILE B1150 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1132 through 1133 removed outlier: 6.995A pdb=" N SER B1132 " --> pdb=" O THR B1198 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR B1184 " --> pdb=" O ILE B1191 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B1193 " --> pdb=" O PHE B1182 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B1181 " --> pdb=" O GLU B1167 " (cutoff:3.500A) 704 hydrogen bonds defined for protein. 1947 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: 8.44 Time building geometry restraints manager: 8.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 3527 1.31 - 1.44: 5482 1.44 - 1.57: 11675 1.57 - 1.71: 0 1.71 - 1.84: 93 Bond restraints: 20777 Sorted by residual: bond pdb=" C PRO B 209 " pdb=" O PRO B 209 " ideal model delta sigma weight residual 1.233 1.172 0.061 1.16e-02 7.43e+03 2.76e+01 bond pdb=" C PRO A1329 " pdb=" O PRO A1329 " ideal model delta sigma weight residual 1.233 1.179 0.054 1.12e-02 7.97e+03 2.32e+01 bond pdb=" CA SER B 233 " pdb=" CB SER B 233 " ideal model delta sigma weight residual 1.527 1.460 0.067 1.44e-02 4.82e+03 2.16e+01 bond pdb=" CA SER B1020 " pdb=" CB SER B1020 " ideal model delta sigma weight residual 1.530 1.463 0.067 1.55e-02 4.16e+03 1.86e+01 bond pdb=" CA SER A1230 " pdb=" CB SER A1230 " ideal model delta sigma weight residual 1.536 1.451 0.085 2.08e-02 2.31e+03 1.66e+01 ... (remaining 20772 not shown) Histogram of bond angle deviations from ideal: 92.95 - 101.34: 41 101.34 - 109.73: 3483 109.73 - 118.11: 12745 118.11 - 126.50: 11695 126.50 - 134.89: 175 Bond angle restraints: 28139 Sorted by residual: angle pdb=" N PRO B 241 " pdb=" CA PRO B 241 " pdb=" CB PRO B 241 " ideal model delta sigma weight residual 103.25 92.95 10.30 1.05e+00 9.07e-01 9.62e+01 angle pdb=" N ARG A1301 " pdb=" CA ARG A1301 " pdb=" C ARG A1301 " ideal model delta sigma weight residual 110.53 102.99 7.54 1.29e+00 6.01e-01 3.42e+01 angle pdb=" N ARG A1301 " pdb=" CA ARG A1301 " pdb=" CB ARG A1301 " ideal model delta sigma weight residual 110.44 118.78 -8.34 1.43e+00 4.89e-01 3.40e+01 angle pdb=" N GLN B 281 " pdb=" CA GLN B 281 " pdb=" C GLN B 281 " ideal model delta sigma weight residual 114.31 107.26 7.05 1.29e+00 6.01e-01 2.99e+01 angle pdb=" N VAL A 84 " pdb=" CA VAL A 84 " pdb=" C VAL A 84 " ideal model delta sigma weight residual 113.71 108.63 5.08 9.50e-01 1.11e+00 2.86e+01 ... (remaining 28134 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 11218 17.88 - 35.76: 1077 35.76 - 53.63: 160 53.63 - 71.51: 31 71.51 - 89.39: 11 Dihedral angle restraints: 12497 sinusoidal: 5033 harmonic: 7464 Sorted by residual: dihedral pdb=" CA ASN B 846 " pdb=" C ASN B 846 " pdb=" N GLU B 847 " pdb=" CA GLU B 847 " ideal model delta harmonic sigma weight residual -180.00 -150.18 -29.82 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA LYS A 964 " pdb=" C LYS A 964 " pdb=" N ASP A 965 " pdb=" CA ASP A 965 " ideal model delta harmonic sigma weight residual 180.00 151.99 28.01 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA PRO B 686 " pdb=" C PRO B 686 " pdb=" N SER B 687 " pdb=" CA SER B 687 " ideal model delta harmonic sigma weight residual 180.00 -152.12 -27.88 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 12494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1574 0.060 - 0.120: 1095 0.120 - 0.181: 409 0.181 - 0.241: 54 0.241 - 0.301: 9 Chirality restraints: 3141 Sorted by residual: chirality pdb=" CA VAL B 823 " pdb=" N VAL B 823 " pdb=" C VAL B 823 " pdb=" CB VAL B 823 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA ILE B 896 " pdb=" N ILE B 896 " pdb=" C ILE B 896 " pdb=" CB ILE B 896 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA PHE B 244 " pdb=" N PHE B 244 " pdb=" C PHE B 244 " pdb=" CB PHE B 244 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 3138 not shown) Planarity restraints: 3624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A1099 " -0.043 2.00e-02 2.50e+03 2.97e-02 1.54e+01 pdb=" CG PHE A1099 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A1099 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A1099 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE A1099 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A1099 " -0.029 2.00e-02 2.50e+03 pdb=" CZ PHE A1099 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 989 " -0.047 2.00e-02 2.50e+03 2.39e-02 1.14e+01 pdb=" CG TYR B 989 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR B 989 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 989 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR B 989 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 989 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 989 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR B 989 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1039 " -0.045 2.00e-02 2.50e+03 2.38e-02 1.14e+01 pdb=" CG TYR B1039 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR B1039 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B1039 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B1039 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B1039 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B1039 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B1039 " -0.022 2.00e-02 2.50e+03 ... (remaining 3621 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1767 2.74 - 3.28: 19591 3.28 - 3.82: 32663 3.82 - 4.36: 46348 4.36 - 4.90: 74298 Nonbonded interactions: 174667 Sorted by model distance: nonbonded pdb=" O LEU B 239 " pdb=" C GLN B 240 " model vdw 2.198 3.270 nonbonded pdb=" O LEU B 93 " pdb=" OG1 THR B 97 " model vdw 2.209 2.440 nonbonded pdb=" O LYS A 813 " pdb=" OG1 THR A 817 " model vdw 2.251 2.440 nonbonded pdb=" O ALA B 111 " pdb=" OG1 THR B 115 " model vdw 2.268 2.440 nonbonded pdb=" OD2 ASP A 243 " pdb=" OG1 THR A 245 " model vdw 2.277 2.440 ... (remaining 174662 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 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: 0.010 Extract box with map and model: 8.110 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 54.280 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 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:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 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 : 0.013 0.085 20777 Z= 0.828 Angle : 1.497 10.297 28139 Z= 1.049 Chirality : 0.083 0.301 3141 Planarity : 0.007 0.057 3624 Dihedral : 14.188 89.389 7688 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.96 % Favored : 91.81 % Rotamer: Outliers : 0.88 % Allowed : 5.92 % Favored : 93.20 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % 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: -4.21 (0.13), residues: 2526 helix: -3.95 (0.11), residues: 638 sheet: -2.36 (0.23), residues: 444 loop : -2.40 (0.14), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.009 TRP B 631 HIS 0.035 0.004 HIS A 922 PHE 0.053 0.007 PHE A1099 TYR 0.050 0.008 TYR A1108 ARG 0.018 0.002 ARG A 766 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 365 time to evaluate : 2.566 Fit side-chains revert: symmetry clash REVERT: A 10 ASN cc_start: 0.8616 (m110) cc_final: 0.8409 (m-40) REVERT: A 46 GLU cc_start: 0.8087 (tt0) cc_final: 0.7793 (tt0) REVERT: A 48 ARG cc_start: 0.6935 (ptp-110) cc_final: 0.6414 (ptp-110) REVERT: A 94 ARG cc_start: 0.7986 (mtm110) cc_final: 0.7758 (mtm-85) REVERT: A 228 SER cc_start: 0.8822 (m) cc_final: 0.8556 (t) REVERT: A 251 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8121 (mm-30) REVERT: A 383 ARG cc_start: 0.7594 (ttp80) cc_final: 0.7176 (ttt-90) REVERT: A 387 ARG cc_start: 0.8569 (ttm170) cc_final: 0.8130 (mtp85) REVERT: A 505 ASP cc_start: 0.7714 (t0) cc_final: 0.7457 (t0) REVERT: A 530 ARG cc_start: 0.7717 (mtt90) cc_final: 0.7172 (mtm110) REVERT: A 554 ASP cc_start: 0.8579 (t70) cc_final: 0.8267 (t0) REVERT: A 576 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6769 (tm) REVERT: A 611 MET cc_start: 0.8574 (mtm) cc_final: 0.8175 (mtt) REVERT: A 615 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7126 (mp0) REVERT: A 645 GLU cc_start: 0.9008 (mp0) cc_final: 0.8745 (mp0) REVERT: A 711 TYR cc_start: 0.6992 (t80) cc_final: 0.6674 (t80) REVERT: A 834 LYS cc_start: 0.8265 (ttmt) cc_final: 0.7868 (tttp) REVERT: A 868 TYR cc_start: 0.8443 (t80) cc_final: 0.7833 (t80) REVERT: A 876 ARG cc_start: 0.8770 (ttp-110) cc_final: 0.8570 (mtm110) REVERT: A 971 LYS cc_start: 0.8436 (ttmt) cc_final: 0.8087 (ttpp) REVERT: A 1209 MET cc_start: 0.6007 (ptt) cc_final: 0.4620 (tmm) REVERT: B 11 ARG cc_start: 0.8205 (ttm170) cc_final: 0.7862 (ttp-170) REVERT: B 107 LYS cc_start: 0.8147 (tppp) cc_final: 0.7692 (ttpt) REVERT: B 151 SER cc_start: 0.8470 (m) cc_final: 0.8233 (t) REVERT: B 207 ARG cc_start: 0.8288 (mtp85) cc_final: 0.7999 (mtm-85) REVERT: B 239 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8306 (tt) REVERT: B 253 LYS cc_start: 0.8094 (ttmt) cc_final: 0.7868 (tttm) REVERT: B 274 GLN cc_start: 0.8950 (mt0) cc_final: 0.8584 (mt0) REVERT: B 425 GLU cc_start: 0.7620 (mp0) cc_final: 0.7271 (mp0) REVERT: B 479 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7509 (pp20) REVERT: B 508 THR cc_start: 0.7368 (t) cc_final: 0.7144 (p) REVERT: B 712 ASN cc_start: 0.8440 (t0) cc_final: 0.8048 (t0) REVERT: B 714 SER cc_start: 0.8546 (t) cc_final: 0.8198 (t) REVERT: B 780 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8509 (mt-10) REVERT: B 900 MET cc_start: 0.7627 (ptp) cc_final: 0.7247 (ptt) REVERT: B 952 GLU cc_start: 0.8171 (mp0) cc_final: 0.7348 (tp30) REVERT: B 1026 MET cc_start: 0.6121 (mtp) cc_final: 0.5919 (mtm) REVERT: B 1053 SER cc_start: 0.8156 (t) cc_final: 0.7424 (p) REVERT: B 1062 LEU cc_start: 0.8355 (mt) cc_final: 0.8118 (mt) REVERT: B 1077 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8445 (tm-30) outliers start: 20 outliers final: 5 residues processed: 377 average time/residue: 1.1858 time to fit residues: 515.7707 Evaluate side-chains 258 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 250 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 241 PRO Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 782 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.7980 chunk 191 optimal weight: 0.6980 chunk 105 optimal weight: 0.0980 chunk 65 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 197 optimal weight: 0.0870 chunk 76 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 228 optimal weight: 2.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 137 GLN A 140 ASN A 158 GLN A 184 ASN A 206 GLN A 303 HIS A 381 ASN A 445 GLN A 534 ASN A 572 HIS A 619 GLN A 632 GLN A 650 GLN A 730 GLN A 819 ASN A 872 GLN A 931 GLN A 955 HIS A1264 ASN B 145 ASN B 212 GLN B 362 GLN B 524 GLN B 570 GLN B 591 ASN B 643 GLN ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 ASN B 777 ASN B 825 HIS B 873 ASN B 908 ASN B1059 ASN B1135 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 20777 Z= 0.152 Angle : 0.523 9.623 28139 Z= 0.286 Chirality : 0.043 0.150 3141 Planarity : 0.004 0.103 3624 Dihedral : 6.019 57.963 2751 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.24 % Favored : 95.65 % Rotamer: Outliers : 2.37 % Allowed : 11.93 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.62 (0.15), residues: 2526 helix: -1.45 (0.18), residues: 641 sheet: -1.86 (0.23), residues: 459 loop : -1.83 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 629 HIS 0.006 0.001 HIS A 922 PHE 0.023 0.001 PHE B 438 TYR 0.017 0.001 TYR A 57 ARG 0.004 0.000 ARG B 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 314 time to evaluate : 2.507 Fit side-chains REVERT: A 10 ASN cc_start: 0.8445 (m110) cc_final: 0.8241 (m-40) REVERT: A 46 GLU cc_start: 0.8023 (tt0) cc_final: 0.7689 (tt0) REVERT: A 48 ARG cc_start: 0.6892 (ptp-110) cc_final: 0.6296 (ptp-110) REVERT: A 381 ASN cc_start: 0.8525 (t0) cc_final: 0.8317 (t0) REVERT: A 383 ARG cc_start: 0.7599 (ttp80) cc_final: 0.7284 (ttt-90) REVERT: A 387 ARG cc_start: 0.8108 (ttm170) cc_final: 0.7752 (ttp80) REVERT: A 447 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8364 (pt) REVERT: A 471 GLN cc_start: 0.8121 (pp30) cc_final: 0.7703 (pp30) REVERT: A 530 ARG cc_start: 0.7536 (mtt90) cc_final: 0.7066 (mtm110) REVERT: A 554 ASP cc_start: 0.8419 (t70) cc_final: 0.8172 (t0) REVERT: A 576 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6728 (tm) REVERT: A 615 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7453 (pt0) REVERT: A 639 ASN cc_start: 0.8676 (m-40) cc_final: 0.8435 (m-40) REVERT: A 645 GLU cc_start: 0.8885 (mp0) cc_final: 0.8673 (mp0) REVERT: A 653 ASP cc_start: 0.6810 (m-30) cc_final: 0.5837 (t0) REVERT: A 711 TYR cc_start: 0.7056 (t80) cc_final: 0.6769 (t80) REVERT: A 834 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7941 (tttt) REVERT: A 868 TYR cc_start: 0.8088 (t80) cc_final: 0.7654 (t80) REVERT: A 876 ARG cc_start: 0.8704 (ttp-110) cc_final: 0.8430 (mtm110) REVERT: A 971 LYS cc_start: 0.8565 (ttmt) cc_final: 0.8139 (tttm) REVERT: A 1209 MET cc_start: 0.5705 (ptt) cc_final: 0.4332 (tmm) REVERT: B 207 ARG cc_start: 0.8327 (mtp85) cc_final: 0.7871 (mtm-85) REVERT: B 253 LYS cc_start: 0.8120 (ttmt) cc_final: 0.7881 (tttm) REVERT: B 274 GLN cc_start: 0.8596 (mt0) cc_final: 0.8344 (mt0) REVERT: B 425 GLU cc_start: 0.7486 (mp0) cc_final: 0.7129 (mp0) REVERT: B 479 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7049 (pp20) REVERT: B 627 MET cc_start: 0.9124 (mtm) cc_final: 0.8805 (mtp) REVERT: B 648 ILE cc_start: 0.7917 (pt) cc_final: 0.7576 (pp) REVERT: B 780 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8322 (mt-10) REVERT: B 900 MET cc_start: 0.7294 (ptp) cc_final: 0.6860 (ptt) REVERT: B 934 ASP cc_start: 0.8482 (m-30) cc_final: 0.8274 (m-30) REVERT: B 952 GLU cc_start: 0.8012 (mp0) cc_final: 0.7329 (tp30) REVERT: B 1053 SER cc_start: 0.8201 (t) cc_final: 0.7484 (p) REVERT: B 1077 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8374 (tm-30) REVERT: B 1099 TYR cc_start: 0.7923 (m-80) cc_final: 0.7695 (m-80) outliers start: 54 outliers final: 19 residues processed: 344 average time/residue: 1.0067 time to fit residues: 407.2421 Evaluate side-chains 268 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 247 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 782 THR Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 986 ASP Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1117 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 229 optimal weight: 6.9990 chunk 247 optimal weight: 7.9990 chunk 204 optimal weight: 5.9990 chunk 227 optimal weight: 0.3980 chunk 78 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 HIS A 303 HIS A 314 HIS A 390 GLN A 450 HIS A 534 ASN A 745 GLN A 952 GLN A1133 HIS A1135 GLN B 127 HIS B 623 ASN B 646 GLN B 688 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 20777 Z= 0.421 Angle : 0.625 9.834 28139 Z= 0.331 Chirality : 0.047 0.185 3141 Planarity : 0.004 0.102 3624 Dihedral : 5.863 58.844 2741 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.45 % Favored : 93.47 % Rotamer: Outliers : 3.99 % Allowed : 14.43 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.09 (0.16), residues: 2526 helix: -0.56 (0.19), residues: 637 sheet: -1.82 (0.22), residues: 498 loop : -1.60 (0.16), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 629 HIS 0.004 0.001 HIS A 893 PHE 0.024 0.002 PHE B 438 TYR 0.023 0.002 TYR A 57 ARG 0.003 0.000 ARG A1189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 254 time to evaluate : 2.487 Fit side-chains revert: symmetry clash REVERT: A 6 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8263 (mmt) REVERT: A 46 GLU cc_start: 0.7984 (tt0) cc_final: 0.7674 (tt0) REVERT: A 48 ARG cc_start: 0.6997 (ptp-110) cc_final: 0.6446 (ptp-110) REVERT: A 135 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7981 (tp30) REVERT: A 447 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8526 (pt) REVERT: A 471 GLN cc_start: 0.8266 (pp30) cc_final: 0.7856 (pp30) REVERT: A 530 ARG cc_start: 0.7641 (mtt90) cc_final: 0.7188 (mtm110) REVERT: A 554 ASP cc_start: 0.8492 (t70) cc_final: 0.8215 (t0) REVERT: A 576 LEU cc_start: 0.7039 (pt) cc_final: 0.6708 (tm) REVERT: A 615 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7587 (pt0) REVERT: A 639 ASN cc_start: 0.8702 (m-40) cc_final: 0.8459 (m-40) REVERT: A 653 ASP cc_start: 0.7040 (m-30) cc_final: 0.6097 (t0) REVERT: A 711 TYR cc_start: 0.7231 (t80) cc_final: 0.7023 (t80) REVERT: A 834 LYS cc_start: 0.8344 (ttmt) cc_final: 0.7954 (tttt) REVERT: A 868 TYR cc_start: 0.8256 (t80) cc_final: 0.7774 (t80) REVERT: A 876 ARG cc_start: 0.8732 (ttp-110) cc_final: 0.8430 (mtm110) REVERT: A 971 LYS cc_start: 0.8552 (ttmt) cc_final: 0.8135 (tttm) REVERT: A 1209 MET cc_start: 0.5843 (ptt) cc_final: 0.4435 (tmm) REVERT: B 11 ARG cc_start: 0.8178 (ttm170) cc_final: 0.7891 (ttp-170) REVERT: B 12 TYR cc_start: 0.8470 (t80) cc_final: 0.8234 (t80) REVERT: B 42 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7142 (mpp) REVERT: B 207 ARG cc_start: 0.8319 (mtp85) cc_final: 0.8072 (mtm-85) REVERT: B 239 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7311 (tt) REVERT: B 253 LYS cc_start: 0.8123 (ttmt) cc_final: 0.7896 (tttm) REVERT: B 274 GLN cc_start: 0.8633 (mt0) cc_final: 0.8360 (mt0) REVERT: B 425 GLU cc_start: 0.7440 (mp0) cc_final: 0.7029 (mp0) REVERT: B 479 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7079 (pp20) REVERT: B 627 MET cc_start: 0.9171 (mtm) cc_final: 0.8897 (mtp) REVERT: B 648 ILE cc_start: 0.7992 (pt) cc_final: 0.7630 (pp) REVERT: B 780 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8466 (mt-10) REVERT: B 900 MET cc_start: 0.7606 (ptp) cc_final: 0.7196 (ptt) REVERT: B 952 GLU cc_start: 0.8069 (mp0) cc_final: 0.7459 (tp30) REVERT: B 1053 SER cc_start: 0.8087 (t) cc_final: 0.7255 (p) REVERT: B 1099 TYR cc_start: 0.7926 (m-80) cc_final: 0.7663 (m-80) REVERT: B 1121 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7183 (tttp) outliers start: 91 outliers final: 29 residues processed: 310 average time/residue: 1.0691 time to fit residues: 389.6359 Evaluate side-chains 269 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 234 time to evaluate : 2.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 782 THR Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 986 ASP Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1121 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 109 optimal weight: 0.1980 chunk 153 optimal weight: 0.7980 chunk 230 optimal weight: 0.8980 chunk 243 optimal weight: 4.9990 chunk 120 optimal weight: 0.2980 chunk 218 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN A 619 GLN B 760 ASN B 863 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 20777 Z= 0.149 Angle : 0.486 8.276 28139 Z= 0.262 Chirality : 0.042 0.160 3141 Planarity : 0.003 0.100 3624 Dihedral : 5.237 57.635 2739 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.43 % Favored : 95.49 % Rotamer: Outliers : 2.85 % Allowed : 16.36 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.48 (0.16), residues: 2526 helix: 0.34 (0.21), residues: 637 sheet: -1.58 (0.22), residues: 500 loop : -1.38 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 629 HIS 0.005 0.001 HIS A 922 PHE 0.019 0.001 PHE B 438 TYR 0.016 0.001 TYR B 576 ARG 0.004 0.000 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 278 time to evaluate : 2.560 Fit side-chains REVERT: A 6 MET cc_start: 0.8584 (mtp) cc_final: 0.8354 (mmt) REVERT: A 46 GLU cc_start: 0.7974 (tt0) cc_final: 0.7486 (tt0) REVERT: A 48 ARG cc_start: 0.6993 (ptp-110) cc_final: 0.6380 (ptp-110) REVERT: A 135 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8056 (tp30) REVERT: A 447 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8221 (pt) REVERT: A 471 GLN cc_start: 0.8171 (pp30) cc_final: 0.7764 (pp30) REVERT: A 530 ARG cc_start: 0.7589 (mtt90) cc_final: 0.7086 (mtm110) REVERT: A 576 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6639 (tm) REVERT: A 615 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7605 (pt0) REVERT: A 639 ASN cc_start: 0.8608 (m-40) cc_final: 0.8372 (m-40) REVERT: A 653 ASP cc_start: 0.6808 (m-30) cc_final: 0.5913 (t0) REVERT: A 711 TYR cc_start: 0.7333 (t80) cc_final: 0.7035 (t80) REVERT: A 768 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8172 (ttp) REVERT: A 776 MET cc_start: 0.8153 (mtp) cc_final: 0.7919 (mtm) REVERT: A 834 LYS cc_start: 0.8242 (ttmt) cc_final: 0.7897 (tptt) REVERT: A 868 TYR cc_start: 0.8150 (t80) cc_final: 0.7655 (t80) REVERT: A 876 ARG cc_start: 0.8706 (ttp-110) cc_final: 0.8381 (mtm110) REVERT: A 952 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8189 (pt0) REVERT: A 971 LYS cc_start: 0.8600 (ttmt) cc_final: 0.8193 (tttm) REVERT: A 1209 MET cc_start: 0.5746 (ptt) cc_final: 0.4337 (tmm) REVERT: A 1321 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7390 (tp30) REVERT: B 11 ARG cc_start: 0.8197 (ttm170) cc_final: 0.7886 (ttp-170) REVERT: B 207 ARG cc_start: 0.8287 (mtp85) cc_final: 0.7777 (mtm-85) REVERT: B 274 GLN cc_start: 0.8559 (mt0) cc_final: 0.8293 (mt0) REVERT: B 344 ASN cc_start: 0.8486 (t0) cc_final: 0.8210 (t0) REVERT: B 425 GLU cc_start: 0.7621 (mp0) cc_final: 0.7247 (mp0) REVERT: B 445 GLN cc_start: 0.8384 (pt0) cc_final: 0.7933 (pt0) REVERT: B 452 MET cc_start: 0.8270 (mmt) cc_final: 0.7870 (mmt) REVERT: B 479 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7233 (pp20) REVERT: B 665 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8192 (p0) REVERT: B 780 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8279 (mt-10) REVERT: B 845 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.7009 (m-30) REVERT: B 900 MET cc_start: 0.7327 (ptp) cc_final: 0.6903 (ptt) REVERT: B 952 GLU cc_start: 0.8095 (mp0) cc_final: 0.7456 (tp30) REVERT: B 1099 TYR cc_start: 0.7958 (m-80) cc_final: 0.7744 (m-80) outliers start: 65 outliers final: 21 residues processed: 313 average time/residue: 1.0899 time to fit residues: 400.5890 Evaluate side-chains 282 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 254 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1307 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 782 THR Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 986 ASP Chi-restraints excluded: chain B residue 1036 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 218 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN A 534 ASN B 127 HIS B 771 ASN B1059 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20777 Z= 0.348 Angle : 0.572 8.339 28139 Z= 0.302 Chirality : 0.046 0.171 3141 Planarity : 0.004 0.099 3624 Dihedral : 5.330 56.373 2737 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.82 % Favored : 94.10 % Rotamer: Outliers : 3.73 % Allowed : 17.06 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.44 (0.16), residues: 2526 helix: 0.36 (0.21), residues: 641 sheet: -1.57 (0.22), residues: 508 loop : -1.34 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 629 HIS 0.004 0.001 HIS A 893 PHE 0.021 0.002 PHE B 438 TYR 0.018 0.002 TYR A 57 ARG 0.003 0.000 ARG A1144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 253 time to evaluate : 2.373 Fit side-chains REVERT: A 6 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8354 (mmt) REVERT: A 83 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6805 (mmm) REVERT: A 135 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8143 (tp30) REVERT: A 447 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8422 (pt) REVERT: A 471 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7849 (pp30) REVERT: A 530 ARG cc_start: 0.7635 (mtt90) cc_final: 0.7188 (mtm110) REVERT: A 576 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6597 (tm) REVERT: A 615 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7692 (pt0) REVERT: A 639 ASN cc_start: 0.8637 (m-40) cc_final: 0.8387 (m-40) REVERT: A 653 ASP cc_start: 0.6989 (m-30) cc_final: 0.6065 (t0) REVERT: A 711 TYR cc_start: 0.7398 (t80) cc_final: 0.7114 (t80) REVERT: A 776 MET cc_start: 0.8263 (mtp) cc_final: 0.7956 (mtm) REVERT: A 834 LYS cc_start: 0.8266 (ttmt) cc_final: 0.7907 (tptt) REVERT: A 868 TYR cc_start: 0.8281 (t80) cc_final: 0.7733 (t80) REVERT: A 876 ARG cc_start: 0.8715 (ttp-110) cc_final: 0.8388 (mtm110) REVERT: A 952 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8275 (pt0) REVERT: A 971 LYS cc_start: 0.8582 (ttmt) cc_final: 0.8175 (tttm) REVERT: A 1209 MET cc_start: 0.5711 (ptt) cc_final: 0.4297 (tmm) REVERT: A 1321 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7433 (tp30) REVERT: B 11 ARG cc_start: 0.8181 (ttm170) cc_final: 0.7882 (ttp-170) REVERT: B 42 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7183 (mpp) REVERT: B 207 ARG cc_start: 0.8286 (mtp85) cc_final: 0.8033 (mtm-85) REVERT: B 235 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7718 (m-40) REVERT: B 239 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7326 (tt) REVERT: B 274 GLN cc_start: 0.8597 (mt0) cc_final: 0.8324 (mt0) REVERT: B 344 ASN cc_start: 0.8441 (t0) cc_final: 0.8098 (t0) REVERT: B 425 GLU cc_start: 0.7587 (mp0) cc_final: 0.7120 (mp0) REVERT: B 445 GLN cc_start: 0.8384 (pt0) cc_final: 0.8133 (pt0) REVERT: B 487 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8214 (mt-10) REVERT: B 648 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7562 (pp) REVERT: B 780 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8432 (mt-10) REVERT: B 845 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7250 (m-30) REVERT: B 900 MET cc_start: 0.7555 (ptp) cc_final: 0.7142 (ptt) REVERT: B 952 GLU cc_start: 0.8063 (mp0) cc_final: 0.7461 (tp30) REVERT: B 1099 TYR cc_start: 0.7967 (m-80) cc_final: 0.7748 (m-80) outliers start: 85 outliers final: 37 residues processed: 298 average time/residue: 1.1083 time to fit residues: 387.4858 Evaluate side-chains 290 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 240 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1307 THR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 127 HIS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 782 THR Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1036 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 143 optimal weight: 0.0970 chunk 60 optimal weight: 4.9990 chunk 243 optimal weight: 10.0000 chunk 202 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN A 390 GLN A 619 GLN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20777 Z= 0.179 Angle : 0.497 7.500 28139 Z= 0.266 Chirality : 0.043 0.210 3141 Planarity : 0.003 0.096 3624 Dihedral : 5.057 59.071 2737 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.51 % Favored : 95.41 % Rotamer: Outliers : 2.72 % Allowed : 18.86 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.16 (0.17), residues: 2526 helix: 0.75 (0.21), residues: 639 sheet: -1.44 (0.22), residues: 509 loop : -1.22 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 629 HIS 0.010 0.001 HIS B 127 PHE 0.018 0.001 PHE B 438 TYR 0.016 0.001 TYR B 576 ARG 0.002 0.000 ARG A1144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 269 time to evaluate : 2.376 Fit side-chains REVERT: A 48 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6459 (ptp-110) REVERT: A 135 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8027 (tp30) REVERT: A 447 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8188 (pt) REVERT: A 471 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7860 (pp30) REVERT: A 530 ARG cc_start: 0.7582 (mtt90) cc_final: 0.7157 (mtm110) REVERT: A 576 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6576 (tm) REVERT: A 615 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7721 (pt0) REVERT: A 639 ASN cc_start: 0.8586 (m-40) cc_final: 0.8348 (m-40) REVERT: A 653 ASP cc_start: 0.6879 (m-30) cc_final: 0.5961 (t0) REVERT: A 711 TYR cc_start: 0.7443 (t80) cc_final: 0.7155 (OUTLIER) REVERT: A 776 MET cc_start: 0.8228 (mtp) cc_final: 0.7939 (mtm) REVERT: A 834 LYS cc_start: 0.8244 (ttmt) cc_final: 0.7884 (tptt) REVERT: A 868 TYR cc_start: 0.8193 (t80) cc_final: 0.7691 (t80) REVERT: A 876 ARG cc_start: 0.8744 (ttp-110) cc_final: 0.8390 (mtm110) REVERT: A 952 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8227 (pt0) REVERT: A 971 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8211 (tttm) REVERT: A 1045 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7761 (ttp-110) REVERT: A 1209 MET cc_start: 0.5707 (ptt) cc_final: 0.4287 (tmm) REVERT: B 11 ARG cc_start: 0.8198 (ttm170) cc_final: 0.7903 (ttp-170) REVERT: B 207 ARG cc_start: 0.8258 (mtp85) cc_final: 0.7900 (mtm-85) REVERT: B 267 LYS cc_start: 0.8050 (ttmm) cc_final: 0.7209 (ttpp) REVERT: B 274 GLN cc_start: 0.8549 (mt0) cc_final: 0.8268 (mt0) REVERT: B 344 ASN cc_start: 0.8418 (t0) cc_final: 0.8061 (t0) REVERT: B 425 GLU cc_start: 0.7625 (mp0) cc_final: 0.7144 (mp0) REVERT: B 445 GLN cc_start: 0.8314 (pt0) cc_final: 0.8034 (pt0) REVERT: B 452 MET cc_start: 0.8337 (mmt) cc_final: 0.7882 (mmt) REVERT: B 648 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7455 (pp) REVERT: B 780 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8261 (mt-10) REVERT: B 845 ASP cc_start: 0.7339 (OUTLIER) cc_final: 0.7065 (m-30) REVERT: B 900 MET cc_start: 0.7345 (ptp) cc_final: 0.6953 (ptt) REVERT: B 952 GLU cc_start: 0.8071 (mp0) cc_final: 0.7467 (tp30) REVERT: B 1077 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8294 (tm-30) REVERT: B 1099 TYR cc_start: 0.7984 (m-80) cc_final: 0.7730 (m-80) outliers start: 62 outliers final: 30 residues processed: 303 average time/residue: 1.0490 time to fit residues: 375.1608 Evaluate side-chains 291 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 253 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1045 ARG Chi-restraints excluded: chain A residue 1307 THR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 782 THR Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1036 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.0870 chunk 27 optimal weight: 0.5980 chunk 138 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 205 optimal weight: 8.9990 chunk 136 optimal weight: 0.7980 chunk 242 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN A 730 GLN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 20777 Z= 0.158 Angle : 0.487 9.036 28139 Z= 0.259 Chirality : 0.042 0.187 3141 Planarity : 0.003 0.093 3624 Dihedral : 4.800 52.719 2737 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.07 % Favored : 94.85 % Rotamer: Outliers : 2.85 % Allowed : 19.43 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.98 (0.17), residues: 2526 helix: 0.93 (0.21), residues: 645 sheet: -1.33 (0.23), residues: 499 loop : -1.13 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 629 HIS 0.005 0.001 HIS A 922 PHE 0.017 0.001 PHE B 438 TYR 0.018 0.001 TYR A1291 ARG 0.006 0.000 ARG A 901 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 283 time to evaluate : 2.226 Fit side-chains REVERT: A 48 ARG cc_start: 0.7131 (ptp-110) cc_final: 0.6494 (ptp-110) REVERT: A 83 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.6669 (mmm) REVERT: A 135 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8013 (tp30) REVERT: A 329 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: A 447 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8080 (pt) REVERT: A 471 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7689 (pp30) REVERT: A 530 ARG cc_start: 0.7602 (mtt90) cc_final: 0.7096 (mtm110) REVERT: A 554 ASP cc_start: 0.8365 (t0) cc_final: 0.8127 (t0) REVERT: A 576 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6609 (tm) REVERT: A 615 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7756 (pt0) REVERT: A 639 ASN cc_start: 0.8526 (m-40) cc_final: 0.8286 (m-40) REVERT: A 653 ASP cc_start: 0.6800 (m-30) cc_final: 0.5922 (t0) REVERT: A 711 TYR cc_start: 0.7513 (t80) cc_final: 0.7227 (OUTLIER) REVERT: A 776 MET cc_start: 0.8239 (mtp) cc_final: 0.7962 (mtm) REVERT: A 834 LYS cc_start: 0.8255 (ttmt) cc_final: 0.7961 (tptt) REVERT: A 868 TYR cc_start: 0.8138 (t80) cc_final: 0.7673 (t80) REVERT: A 876 ARG cc_start: 0.8714 (ttp-110) cc_final: 0.8356 (mtm110) REVERT: A 958 GLN cc_start: 0.8240 (tt0) cc_final: 0.7704 (tt0) REVERT: A 971 LYS cc_start: 0.8647 (ttmt) cc_final: 0.8248 (tttm) REVERT: A 1035 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8529 (tt0) REVERT: A 1045 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7764 (ttp-110) REVERT: A 1138 TYR cc_start: 0.8967 (m-80) cc_final: 0.8684 (m-80) REVERT: A 1209 MET cc_start: 0.5651 (ptt) cc_final: 0.4316 (tmm) REVERT: A 1264 ASN cc_start: 0.8203 (m-40) cc_final: 0.7998 (m-40) REVERT: B 11 ARG cc_start: 0.8198 (ttm170) cc_final: 0.7900 (ttp-170) REVERT: B 60 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8001 (pt) REVERT: B 156 ASN cc_start: 0.8218 (t0) cc_final: 0.7883 (t0) REVERT: B 267 LYS cc_start: 0.8054 (ttmm) cc_final: 0.7239 (ttpp) REVERT: B 274 GLN cc_start: 0.8535 (mt0) cc_final: 0.8249 (mt0) REVERT: B 344 ASN cc_start: 0.8380 (t0) cc_final: 0.8006 (t0) REVERT: B 425 GLU cc_start: 0.7603 (mp0) cc_final: 0.7181 (mp0) REVERT: B 452 MET cc_start: 0.8344 (mmt) cc_final: 0.7897 (mmt) REVERT: B 648 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7344 (pp) REVERT: B 665 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8261 (p0) REVERT: B 780 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8208 (mt-10) REVERT: B 845 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.7020 (m-30) REVERT: B 847 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7849 (mp0) REVERT: B 900 MET cc_start: 0.7218 (ptp) cc_final: 0.6810 (ptt) REVERT: B 952 GLU cc_start: 0.8056 (mp0) cc_final: 0.7447 (tp30) outliers start: 65 outliers final: 28 residues processed: 322 average time/residue: 1.0044 time to fit residues: 383.4934 Evaluate side-chains 297 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 258 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1035 GLU Chi-restraints excluded: chain A residue 1045 ARG Chi-restraints excluded: chain A residue 1307 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 782 THR Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 1036 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 220 optimal weight: 0.0030 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN A 390 GLN A 619 GLN A 730 GLN A 952 GLN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 865 ASN B1035 ASN B1059 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 20777 Z= 0.378 Angle : 0.598 11.302 28139 Z= 0.312 Chirality : 0.047 0.276 3141 Planarity : 0.004 0.092 3624 Dihedral : 5.252 56.481 2737 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.10 % Favored : 93.82 % Rotamer: Outliers : 3.25 % Allowed : 19.17 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.13 (0.17), residues: 2526 helix: 0.72 (0.21), residues: 637 sheet: -1.40 (0.23), residues: 498 loop : -1.19 (0.16), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1141 HIS 0.004 0.001 HIS A 893 PHE 0.020 0.002 PHE B 438 TYR 0.022 0.002 TYR A 108 ARG 0.005 0.000 ARG A 901 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 238 time to evaluate : 2.399 Fit side-chains REVERT: A 48 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6425 (ptp-110) REVERT: A 135 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8146 (tp30) REVERT: A 329 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7756 (mp0) REVERT: A 447 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8364 (pt) REVERT: A 467 VAL cc_start: 0.8493 (t) cc_final: 0.8290 (t) REVERT: A 471 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7617 (pp30) REVERT: A 530 ARG cc_start: 0.7668 (mtt90) cc_final: 0.7213 (mtm110) REVERT: A 554 ASP cc_start: 0.8414 (t0) cc_final: 0.8158 (t0) REVERT: A 597 LYS cc_start: 0.8920 (mttm) cc_final: 0.8594 (mttm) REVERT: A 615 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7830 (pt0) REVERT: A 653 ASP cc_start: 0.7018 (m-30) cc_final: 0.6099 (t0) REVERT: A 711 TYR cc_start: 0.7633 (t80) cc_final: 0.7354 (t80) REVERT: A 776 MET cc_start: 0.8296 (mtp) cc_final: 0.7980 (mtm) REVERT: A 834 LYS cc_start: 0.8307 (ttmt) cc_final: 0.7928 (tptt) REVERT: A 868 TYR cc_start: 0.8304 (t80) cc_final: 0.7869 (t80) REVERT: A 958 GLN cc_start: 0.8334 (tt0) cc_final: 0.7762 (tt0) REVERT: A 971 LYS cc_start: 0.8623 (ttmt) cc_final: 0.8211 (tttm) REVERT: A 1045 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7855 (ttp-110) REVERT: A 1209 MET cc_start: 0.5660 (ptt) cc_final: 0.4355 (tmm) REVERT: B 207 ARG cc_start: 0.8270 (mtp85) cc_final: 0.7956 (mtm-85) REVERT: B 235 ASN cc_start: 0.8029 (OUTLIER) cc_final: 0.7769 (m-40) REVERT: B 253 LYS cc_start: 0.8132 (ttmt) cc_final: 0.7882 (tttm) REVERT: B 263 ILE cc_start: 0.7629 (tp) cc_final: 0.7366 (tt) REVERT: B 267 LYS cc_start: 0.8054 (ttmm) cc_final: 0.7216 (ttpp) REVERT: B 274 GLN cc_start: 0.8607 (mt0) cc_final: 0.8324 (mt0) REVERT: B 344 ASN cc_start: 0.8426 (t0) cc_final: 0.8038 (t0) REVERT: B 425 GLU cc_start: 0.7547 (mp0) cc_final: 0.7115 (mp0) REVERT: B 780 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8385 (mt-10) REVERT: B 845 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7162 (m-30) REVERT: B 900 MET cc_start: 0.7513 (ptp) cc_final: 0.7112 (ptt) REVERT: B 952 GLU cc_start: 0.8079 (mp0) cc_final: 0.7453 (tp30) REVERT: B 1077 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8476 (tm-30) outliers start: 74 outliers final: 36 residues processed: 285 average time/residue: 1.0921 time to fit residues: 365.2507 Evaluate side-chains 278 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 234 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1045 ARG Chi-restraints excluded: chain A residue 1307 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 646 GLN Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 698 ASN Chi-restraints excluded: chain B residue 782 THR Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 1035 ASN Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1086 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 177 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 225 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN A 952 GLN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20777 Z= 0.252 Angle : 0.537 9.757 28139 Z= 0.283 Chirality : 0.044 0.223 3141 Planarity : 0.003 0.090 3624 Dihedral : 5.108 54.741 2737 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.70 % Rotamer: Outliers : 2.50 % Allowed : 20.22 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.17), residues: 2526 helix: 0.84 (0.21), residues: 637 sheet: -1.36 (0.23), residues: 478 loop : -1.16 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 629 HIS 0.003 0.001 HIS A 893 PHE 0.018 0.001 PHE B 438 TYR 0.017 0.002 TYR A 108 ARG 0.007 0.000 ARG A 901 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 241 time to evaluate : 2.833 Fit side-chains REVERT: A 48 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6466 (ptp-110) REVERT: A 135 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8113 (tp30) REVERT: A 329 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: A 447 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8242 (pt) REVERT: A 470 MET cc_start: 0.7806 (ptp) cc_final: 0.7479 (mtm) REVERT: A 471 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7725 (pp30) REVERT: A 530 ARG cc_start: 0.7621 (mtt90) cc_final: 0.7176 (mtm110) REVERT: A 554 ASP cc_start: 0.8423 (t0) cc_final: 0.8166 (t0) REVERT: A 615 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7699 (pt0) REVERT: A 653 ASP cc_start: 0.6962 (m-30) cc_final: 0.6025 (t0) REVERT: A 711 TYR cc_start: 0.7636 (t80) cc_final: 0.7368 (t80) REVERT: A 776 MET cc_start: 0.8235 (mtp) cc_final: 0.7982 (mtm) REVERT: A 834 LYS cc_start: 0.8259 (ttmt) cc_final: 0.7897 (tptt) REVERT: A 868 TYR cc_start: 0.8236 (t80) cc_final: 0.7776 (t80) REVERT: A 958 GLN cc_start: 0.8282 (tt0) cc_final: 0.7717 (tt0) REVERT: A 971 LYS cc_start: 0.8647 (ttmt) cc_final: 0.8236 (tttm) REVERT: A 1045 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7809 (ttp-110) REVERT: A 1209 MET cc_start: 0.5595 (ptt) cc_final: 0.4379 (tmm) REVERT: B 11 ARG cc_start: 0.8138 (ttm170) cc_final: 0.7771 (ttp-170) REVERT: B 42 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7036 (mpp) REVERT: B 207 ARG cc_start: 0.8255 (mtp85) cc_final: 0.7895 (mtm-85) REVERT: B 267 LYS cc_start: 0.8061 (ttmm) cc_final: 0.7225 (ttpp) REVERT: B 274 GLN cc_start: 0.8580 (mt0) cc_final: 0.8291 (mt0) REVERT: B 344 ASN cc_start: 0.8397 (t0) cc_final: 0.8011 (t0) REVERT: B 425 GLU cc_start: 0.7574 (mp0) cc_final: 0.7071 (mp0) REVERT: B 648 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7362 (pp) REVERT: B 780 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8359 (mt-10) REVERT: B 845 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.7107 (m-30) REVERT: B 900 MET cc_start: 0.7432 (ptp) cc_final: 0.7029 (ptt) REVERT: B 952 GLU cc_start: 0.8010 (mp0) cc_final: 0.7393 (tp30) REVERT: B 1077 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8413 (tm-30) REVERT: B 1121 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7150 (tttp) outliers start: 57 outliers final: 30 residues processed: 276 average time/residue: 1.0831 time to fit residues: 354.1271 Evaluate side-chains 277 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 237 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1045 ARG Chi-restraints excluded: chain A residue 1307 THR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 698 ASN Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 782 THR Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1086 SER Chi-restraints excluded: chain B residue 1121 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 251 optimal weight: 4.9990 chunk 231 optimal weight: 0.0870 chunk 199 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 122 optimal weight: 0.0060 chunk 158 optimal weight: 0.0980 overall best weight: 0.8376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN ** A 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 GLN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20777 Z= 0.174 Angle : 0.499 7.514 28139 Z= 0.264 Chirality : 0.043 0.192 3141 Planarity : 0.003 0.048 3624 Dihedral : 4.871 48.262 2737 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.11 % Favored : 94.85 % Rotamer: Outliers : 2.19 % Allowed : 20.66 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.32 % 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: -0.85 (0.17), residues: 2526 helix: 1.06 (0.21), residues: 638 sheet: -1.30 (0.23), residues: 485 loop : -1.05 (0.16), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 629 HIS 0.004 0.001 HIS A 922 PHE 0.017 0.001 PHE B 438 TYR 0.017 0.001 TYR A 518 ARG 0.006 0.000 ARG A 901 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 264 time to evaluate : 2.552 Fit side-chains REVERT: A 48 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6456 (ptp-110) REVERT: A 135 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7990 (tp30) REVERT: A 329 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: A 447 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8086 (pt) REVERT: A 471 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7632 (pp30) REVERT: A 530 ARG cc_start: 0.7650 (mtt90) cc_final: 0.7203 (mtm110) REVERT: A 554 ASP cc_start: 0.8383 (t0) cc_final: 0.8148 (t0) REVERT: A 576 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6803 (tm) REVERT: A 615 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7664 (pt0) REVERT: A 653 ASP cc_start: 0.6835 (m-30) cc_final: 0.5960 (t0) REVERT: A 711 TYR cc_start: 0.7659 (t80) cc_final: 0.7418 (t80) REVERT: A 776 MET cc_start: 0.8193 (mtp) cc_final: 0.7991 (mtm) REVERT: A 834 LYS cc_start: 0.8245 (ttmt) cc_final: 0.7895 (tptt) REVERT: A 868 TYR cc_start: 0.8124 (t80) cc_final: 0.7658 (t80) REVERT: A 971 LYS cc_start: 0.8665 (ttmt) cc_final: 0.8267 (tttm) REVERT: A 1045 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7774 (ttp-110) REVERT: A 1169 LYS cc_start: 0.8854 (mttp) cc_final: 0.8302 (mtpt) REVERT: A 1209 MET cc_start: 0.5535 (ptt) cc_final: 0.4397 (tmm) REVERT: B 42 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7178 (mpp) REVERT: B 156 ASN cc_start: 0.8251 (t0) cc_final: 0.7898 (t0) REVERT: B 207 ARG cc_start: 0.8258 (mtp85) cc_final: 0.7718 (mtm-85) REVERT: B 235 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.7775 (m-40) REVERT: B 267 LYS cc_start: 0.8047 (ttmm) cc_final: 0.7241 (ttpp) REVERT: B 274 GLN cc_start: 0.8563 (mt0) cc_final: 0.8274 (mt0) REVERT: B 344 ASN cc_start: 0.8367 (t0) cc_final: 0.7985 (t0) REVERT: B 425 GLU cc_start: 0.7575 (mp0) cc_final: 0.7141 (mp0) REVERT: B 452 MET cc_start: 0.8352 (mmt) cc_final: 0.7944 (mmt) REVERT: B 648 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7271 (pp) REVERT: B 780 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8345 (mt-10) REVERT: B 845 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.7001 (m-30) REVERT: B 847 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7814 (mp0) REVERT: B 900 MET cc_start: 0.7253 (ptp) cc_final: 0.6858 (ptt) REVERT: B 952 GLU cc_start: 0.8022 (mp0) cc_final: 0.7424 (tp30) outliers start: 50 outliers final: 26 residues processed: 291 average time/residue: 1.0356 time to fit residues: 355.2162 Evaluate side-chains 288 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 251 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1045 ARG Chi-restraints excluded: chain A residue 1307 THR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 1036 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 205 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN ** A 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 GLN A1079 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1035 ASN B1059 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.146733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.119727 restraints weight = 24128.081| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.82 r_work: 0.3281 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20777 Z= 0.280 Angle : 0.554 9.351 28139 Z= 0.290 Chirality : 0.045 0.217 3141 Planarity : 0.003 0.045 3624 Dihedral : 4.991 36.324 2736 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.97 % Allowed : 21.14 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.32 % 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: -0.91 (0.17), residues: 2526 helix: 0.97 (0.21), residues: 635 sheet: -1.30 (0.23), residues: 496 loop : -1.06 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 629 HIS 0.004 0.001 HIS A 893 PHE 0.018 0.002 PHE B 438 TYR 0.017 0.002 TYR A1291 ARG 0.007 0.000 ARG A 901 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7072.78 seconds wall clock time: 127 minutes 13.57 seconds (7633.57 seconds total)