Starting phenix.real_space_refine on Tue Mar 19 12:02:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sje_10215/03_2024/6sje_10215.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sje_10215/03_2024/6sje_10215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sje_10215/03_2024/6sje_10215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sje_10215/03_2024/6sje_10215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sje_10215/03_2024/6sje_10215.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sje_10215/03_2024/6sje_10215.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 68 5.49 5 S 101 5.16 5 C 15036 2.51 5 N 4236 2.21 5 O 4674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 119": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 330": "NH1" <-> "NH2" Residue "B ARG 341": "NH1" <-> "NH2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B ARG 547": "NH1" <-> "NH2" Residue "B ARG 561": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 653": "NH1" <-> "NH2" Residue "B ARG 655": "NH1" <-> "NH2" Residue "B ARG 662": "NH1" <-> "NH2" Residue "B ARG 682": "NH1" <-> "NH2" Residue "B ARG 683": "NH1" <-> "NH2" Residue "B ARG 728": "NH1" <-> "NH2" Residue "B ARG 761": "NH1" <-> "NH2" Residue "B ARG 771": "NH1" <-> "NH2" Residue "B ARG 840": "NH1" <-> "NH2" Residue "B ARG 895": "NH1" <-> "NH2" Residue "B PHE 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1015": "NH1" <-> "NH2" Residue "B ARG 1106": "NH1" <-> "NH2" Residue "B TYR 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1120": "NH1" <-> "NH2" Residue "B PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 9": "NH1" <-> "NH2" Residue "C ARG 23": "NH1" <-> "NH2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 112": "NH1" <-> "NH2" Residue "C TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "C TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 348": "NH1" <-> "NH2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ARG 392": "NH1" <-> "NH2" Residue "C ARG 433": "NH1" <-> "NH2" Residue "C ARG 443": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 525": "NH1" <-> "NH2" Residue "C ARG 530": "NH1" <-> "NH2" Residue "C ARG 575": "NH1" <-> "NH2" Residue "C ARG 592": "NH1" <-> "NH2" Residue "C TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 649": "NH1" <-> "NH2" Residue "C PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 668": "NH1" <-> "NH2" Residue "C ARG 687": "NH1" <-> "NH2" Residue "C ARG 703": "NH1" <-> "NH2" Residue "C ARG 706": "NH1" <-> "NH2" Residue "C ARG 708": "NH1" <-> "NH2" Residue "C ARG 709": "NH1" <-> "NH2" Residue "C ARG 742": "NH1" <-> "NH2" Residue "C ARG 799": "NH1" <-> "NH2" Residue "C ARG 839": "NH1" <-> "NH2" Residue "C PHE 849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 877": "NH1" <-> "NH2" Residue "C TYR 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 896": "NH1" <-> "NH2" Residue "C ARG 900": "NH1" <-> "NH2" Residue "C ARG 902": "NH1" <-> "NH2" Residue "C ARG 966": "NH1" <-> "NH2" Residue "C ARG 1001": "NH1" <-> "NH2" Residue "C ARG 1007": "NH1" <-> "NH2" Residue "C ARG 1118": "NH1" <-> "NH2" Residue "C PHE 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 252": "NH1" <-> "NH2" Residue "D ARG 281": "NH1" <-> "NH2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "D PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 396": "NH1" <-> "NH2" Residue "D ARG 417": "NH1" <-> "NH2" Residue "D ARG 470": "NH1" <-> "NH2" Residue "D ARG 475": "NH1" <-> "NH2" Residue "D PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 509": "NH1" <-> "NH2" Residue "D PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 526": "NH1" <-> "NH2" Residue "D ARG 557": "NH1" <-> "NH2" Residue "D ARG 574": "NH1" <-> "NH2" Residue "D ARG 576": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24115 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9047 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 51, 'TRANS': 1077} Chain breaks: 2 Chain: "C" Number of atoms: 9078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 9078 Classifications: {'peptide': 1121} Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1053} Chain: "D" Number of atoms: 4603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4603 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 25, 'TRANS': 571} Chain: "X" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1387 Classifications: {'DNA': 68} Link IDs: {'rna3p': 67} Chain breaks: 1 Time building chain proxies: 12.16, per 1000 atoms: 0.50 Number of scatterers: 24115 At special positions: 0 Unit cell: (151.815, 149.721, 124.593, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 101 16.00 P 68 15.00 O 4674 8.00 N 4236 7.00 C 15036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 8.97 Conformation dependent library (CDL) restraints added in 4.1 seconds 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5372 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 16 sheets defined 53.8% alpha, 9.6% beta 17 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 8.11 Creating SS restraints... Processing helix chain 'B' and resid 28 through 43 Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.678A pdb=" N LEU B 59 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 90 Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.743A pdb=" N ILE B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 121 through 124 Processing helix chain 'B' and resid 128 through 140 Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.546A pdb=" N SER B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 173 removed outlier: 3.841A pdb=" N TYR B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.261A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 3.780A pdb=" N LEU B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 239 removed outlier: 3.566A pdb=" N VAL B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 275 through 281 removed outlier: 3.675A pdb=" N ASN B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.725A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 317 removed outlier: 4.169A pdb=" N GLU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 4.546A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.584A pdb=" N MET B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 378 Processing helix chain 'B' and resid 390 through 401 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.758A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.764A pdb=" N TYR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 461 Processing helix chain 'B' and resid 511 through 534 removed outlier: 3.568A pdb=" N GLN B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 573 removed outlier: 3.519A pdb=" N ALA B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 573 " --> pdb=" O ASP B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 removed outlier: 3.636A pdb=" N GLU B 589 " --> pdb=" O SER B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 586 through 589' Processing helix chain 'B' and resid 590 through 605 removed outlier: 3.872A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.969A pdb=" N LEU B 612 " --> pdb=" O ARG B 608 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 617 " --> pdb=" O ARG B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 634 Processing helix chain 'B' and resid 634 through 655 removed outlier: 3.569A pdb=" N TRP B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 668 removed outlier: 3.821A pdb=" N MET B 660 " --> pdb=" O GLY B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 677 removed outlier: 3.528A pdb=" N ASN B 673 " --> pdb=" O ASN B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 699 Processing helix chain 'B' and resid 704 through 717 removed outlier: 3.767A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 807 removed outlier: 3.586A pdb=" N GLU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 836 Processing helix chain 'B' and resid 837 through 843 removed outlier: 4.002A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 860 removed outlier: 3.902A pdb=" N LEU B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 910 Processing helix chain 'B' and resid 941 through 945 Processing helix chain 'B' and resid 948 through 962 Processing helix chain 'B' and resid 969 through 981 Processing helix chain 'B' and resid 986 through 1000 removed outlier: 3.699A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1012 removed outlier: 3.782A pdb=" N GLN B1011 " --> pdb=" O SER B1008 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B1012 " --> pdb=" O LEU B1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1008 through 1012' Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 3.672A pdb=" N THR B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1048 removed outlier: 3.890A pdb=" N ALA B1048 " --> pdb=" O PRO B1045 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1045 through 1048' Processing helix chain 'B' and resid 1094 through 1106 Processing helix chain 'B' and resid 1107 through 1126 Processing helix chain 'B' and resid 1130 through 1134 Processing helix chain 'B' and resid 1144 through 1146 No H-bonds generated for 'chain 'B' and resid 1144 through 1146' Processing helix chain 'B' and resid 1163 through 1174 removed outlier: 3.668A pdb=" N LEU B1167 " --> pdb=" O GLY B1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.907A pdb=" N LEU C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 55 Processing helix chain 'C' and resid 64 through 77 Processing helix chain 'C' and resid 87 through 99 removed outlier: 3.664A pdb=" N THR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 116 removed outlier: 3.792A pdb=" N HIS C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 142 Processing helix chain 'C' and resid 142 through 152 removed outlier: 3.729A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 179 Processing helix chain 'C' and resid 185 through 199 Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.556A pdb=" N ALA C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.670A pdb=" N PHE C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 333 through 344 Processing helix chain 'C' and resid 354 through 360 Processing helix chain 'C' and resid 381 through 400 Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 418 through 428 Processing helix chain 'C' and resid 447 through 459 removed outlier: 3.642A pdb=" N GLU C 452 " --> pdb=" O HIS C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 472 Processing helix chain 'C' and resid 476 through 483 removed outlier: 3.589A pdb=" N PHE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.868A pdb=" N GLN C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 removed outlier: 3.535A pdb=" N LEU C 514 " --> pdb=" O ASN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 537 Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.827A pdb=" N GLN C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 599 removed outlier: 4.468A pdb=" N CYS C 591 " --> pdb=" O TRP C 587 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 625 Processing helix chain 'C' and resid 633 through 646 removed outlier: 4.020A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 700 removed outlier: 3.885A pdb=" N GLN C 699 " --> pdb=" O ASP C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 723 Processing helix chain 'C' and resid 745 through 758 Processing helix chain 'C' and resid 769 through 780 Processing helix chain 'C' and resid 806 through 812 Processing helix chain 'C' and resid 833 through 843 removed outlier: 3.568A pdb=" N LEU C 837 " --> pdb=" O PRO C 833 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS C 843 " --> pdb=" O ARG C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 851 Processing helix chain 'C' and resid 874 through 889 Processing helix chain 'C' and resid 893 through 904 removed outlier: 3.630A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 932 removed outlier: 3.799A pdb=" N GLU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 935 No H-bonds generated for 'chain 'C' and resid 933 through 935' Processing helix chain 'C' and resid 973 through 989 removed outlier: 3.542A pdb=" N GLY C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1033 removed outlier: 4.017A pdb=" N SER C1032 " --> pdb=" O ARG C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1050 Processing helix chain 'C' and resid 1060 through 1076 removed outlier: 3.639A pdb=" N ARG C1068 " --> pdb=" O LEU C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1113 Processing helix chain 'C' and resid 1113 through 1119 removed outlier: 3.823A pdb=" N PHE C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.580A pdb=" N GLN D 15 " --> pdb=" O VAL D 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 11 through 15' Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 32 through 49 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 80 through 88 removed outlier: 3.957A pdb=" N SER D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 125 Processing helix chain 'D' and resid 133 through 145 Processing helix chain 'D' and resid 152 through 164 removed outlier: 3.547A pdb=" N ARG D 164 " --> pdb=" O VAL D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 192 Processing helix chain 'D' and resid 205 through 221 removed outlier: 3.526A pdb=" N ARG D 221 " --> pdb=" O GLY D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 232 removed outlier: 3.571A pdb=" N LYS D 231 " --> pdb=" O ASP D 227 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 245 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.610A pdb=" N MET D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 285 removed outlier: 3.510A pdb=" N ALA D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 315 removed outlier: 3.770A pdb=" N ASP D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 319 removed outlier: 3.554A pdb=" N ALA D 319 " --> pdb=" O TYR D 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 316 through 319' Processing helix chain 'D' and resid 322 through 334 removed outlier: 3.618A pdb=" N ARG D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 352 Processing helix chain 'D' and resid 365 through 375 removed outlier: 3.940A pdb=" N GLN D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.641A pdb=" N ALA D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN D 387 " --> pdb=" O LYS D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 391 removed outlier: 3.856A pdb=" N THR D 391 " --> pdb=" O GLN D 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 388 through 391' Processing helix chain 'D' and resid 400 through 415 Processing helix chain 'D' and resid 415 through 424 Processing helix chain 'D' and resid 427 through 436 removed outlier: 3.587A pdb=" N ILE D 431 " --> pdb=" O GLU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 465 Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.528A pdb=" N LEU D 527 " --> pdb=" O PRO D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 571 Processing helix chain 'D' and resid 582 through 592 removed outlier: 3.695A pdb=" N ILE D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA D 591 " --> pdb=" O SER D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 604 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 6.362A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA B 439 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 20 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLY B 17 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU B 411 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL B 62 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL B 61 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 152 removed outlier: 6.520A pdb=" N GLN B 151 " --> pdb=" O LEU B 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 207 through 208 removed outlier: 6.370A pdb=" N VAL B 207 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA5, first strand: chain 'B' and resid 487 through 490 Processing sheet with id=AA6, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.701A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE B 554 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N VAL B 739 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 901 through 904 removed outlier: 6.262A pdb=" N ARG B 902 " --> pdb=" O MET B1061 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LYS B1063 " --> pdb=" O ARG B 902 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B 904 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N PHE B1065 " --> pdb=" O THR B 904 " (cutoff:3.500A) removed outlier: 10.181A pdb=" N ILE B1066 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N TYR B1081 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR B1076 " --> pdb=" O PHE B1135 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY B1137 " --> pdb=" O TYR B1076 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 901 through 904 removed outlier: 6.262A pdb=" N ARG B 902 " --> pdb=" O MET B1061 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LYS B1063 " --> pdb=" O ARG B 902 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B 904 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N PHE B1065 " --> pdb=" O THR B 904 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU B1068 " --> pdb=" O VAL B1019 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B1019 " --> pdb=" O LEU B1068 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE B1070 " --> pdb=" O LYS B1017 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LYS B1017 " --> pdb=" O PHE B1070 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA C 57 " --> pdb=" O TYR B1024 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 34 through 36 removed outlier: 4.460A pdb=" N MET C 34 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ARG C 3 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE C 240 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N TYR C 5 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG C 266 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.020A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 437 through 439 removed outlier: 7.273A pdb=" N ILE C 408 " --> pdb=" O ASN C 660 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N CYS C 662 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL C 410 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N THR C 375 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N TYR C 731 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N HIS C 377 " --> pdb=" O TYR C 731 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N CYS C 782 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N PHE C 376 " --> pdb=" O CYS C 782 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 939 through 947 removed outlier: 5.469A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 15.483A pdb=" N LEU C 956 " --> pdb=" O TRP C 967 " (cutoff:3.500A) removed outlier: 13.158A pdb=" N TRP C 967 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLN C 958 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU C 965 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.039A pdb=" N SER D 92 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 167 through 170 removed outlier: 6.604A pdb=" N ARG D 200 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N SER D 238 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU D 201 " --> pdb=" O SER D 238 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 393 through 396 removed outlier: 7.236A pdb=" N ASP D 547 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU D 440 " --> pdb=" O MET D 536 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 519 through 522 removed outlier: 4.561A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) 1064 hydrogen bonds defined for protein. 3117 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 9.30 Time building geometry restraints manager: 9.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6608 1.33 - 1.45: 4535 1.45 - 1.57: 13328 1.57 - 1.69: 134 1.69 - 1.81: 169 Bond restraints: 24774 Sorted by residual: bond pdb=" C ASN C 660 " pdb=" N ILE C 661 " ideal model delta sigma weight residual 1.330 1.246 0.084 1.25e-02 6.40e+03 4.53e+01 bond pdb=" C LEU C 588 " pdb=" N PRO C 589 " ideal model delta sigma weight residual 1.331 1.376 -0.045 7.90e-03 1.60e+04 3.20e+01 bond pdb=" O3' DC X 80 " pdb=" P DT X 81 " ideal model delta sigma weight residual 1.607 1.681 -0.074 1.50e-02 4.44e+03 2.41e+01 bond pdb=" P DT X 81 " pdb=" OP1 DT X 81 " ideal model delta sigma weight residual 1.480 1.553 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" CA LEU C 664 " pdb=" C LEU C 664 " ideal model delta sigma weight residual 1.523 1.561 -0.037 1.30e-02 5.92e+03 8.20e+00 ... (remaining 24769 not shown) Histogram of bond angle deviations from ideal: 99.42 - 106.34: 1121 106.34 - 113.27: 13072 113.27 - 120.20: 9284 120.20 - 127.12: 10009 127.12 - 134.05: 422 Bond angle restraints: 33908 Sorted by residual: angle pdb=" N LEU C 664 " pdb=" CA LEU C 664 " pdb=" C LEU C 664 " ideal model delta sigma weight residual 111.28 122.86 -11.58 1.09e+00 8.42e-01 1.13e+02 angle pdb=" N MET C 665 " pdb=" CA MET C 665 " pdb=" C MET C 665 " ideal model delta sigma weight residual 113.16 123.91 -10.75 1.42e+00 4.96e-01 5.73e+01 angle pdb=" C PHE B 468 " pdb=" N MET B 469 " pdb=" CA MET B 469 " ideal model delta sigma weight residual 121.54 130.01 -8.47 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C2' DC X 80 " pdb=" C1' DC X 80 " pdb=" N1 DC X 80 " ideal model delta sigma weight residual 113.50 119.69 -6.19 1.50e+00 4.44e-01 1.71e+01 angle pdb=" O3' DC X 80 " pdb=" C3' DC X 80 " pdb=" C2' DC X 80 " ideal model delta sigma weight residual 111.50 117.44 -5.94 1.50e+00 4.44e-01 1.57e+01 ... (remaining 33903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 13467 17.11 - 34.22: 826 34.22 - 51.33: 368 51.33 - 68.44: 85 68.44 - 85.55: 9 Dihedral angle restraints: 14755 sinusoidal: 6466 harmonic: 8289 Sorted by residual: dihedral pdb=" CA PRO B1051 " pdb=" C PRO B1051 " pdb=" N PRO B1052 " pdb=" CA PRO B1052 " ideal model delta harmonic sigma weight residual -180.00 -162.06 -17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" N MET C 665 " pdb=" C MET C 665 " pdb=" CA MET C 665 " pdb=" CB MET C 665 " ideal model delta harmonic sigma weight residual 122.80 131.61 -8.81 0 2.50e+00 1.60e-01 1.24e+01 dihedral pdb=" C MET C 665 " pdb=" N MET C 665 " pdb=" CA MET C 665 " pdb=" CB MET C 665 " ideal model delta harmonic sigma weight residual -122.60 -131.32 8.72 0 2.50e+00 1.60e-01 1.22e+01 ... (remaining 14752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 3569 0.094 - 0.188: 154 0.188 - 0.282: 3 0.282 - 0.376: 2 0.376 - 0.470: 1 Chirality restraints: 3729 Sorted by residual: chirality pdb=" CA MET C 665 " pdb=" N MET C 665 " pdb=" C MET C 665 " pdb=" CB MET C 665 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.52e+00 chirality pdb=" P DT X 81 " pdb=" OP1 DT X 81 " pdb=" OP2 DT X 81 " pdb=" O5' DT X 81 " both_signs ideal model delta sigma weight residual True 2.35 -2.65 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA LEU C 664 " pdb=" N LEU C 664 " pdb=" C LEU C 664 " pdb=" CB LEU C 664 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 3726 not shown) Planarity restraints: 4219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 419 " -0.040 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO C 420 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 420 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 420 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 304 " 0.038 5.00e-02 4.00e+02 5.60e-02 5.01e+00 pdb=" N PRO B 305 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 305 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 305 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG X 83 " -0.025 2.00e-02 2.50e+03 1.17e-02 4.09e+00 pdb=" N9 DG X 83 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DG X 83 " 0.013 2.00e-02 2.50e+03 pdb=" N7 DG X 83 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG X 83 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG X 83 " 0.000 2.00e-02 2.50e+03 pdb=" O6 DG X 83 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DG X 83 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG X 83 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG X 83 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DG X 83 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DG X 83 " -0.009 2.00e-02 2.50e+03 ... (remaining 4216 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5611 2.79 - 3.32: 20052 3.32 - 3.85: 40337 3.85 - 4.37: 45746 4.37 - 4.90: 77972 Nonbonded interactions: 189718 Sorted by model distance: nonbonded pdb=" O PHE C 62 " pdb=" N1 DG X 86 " model vdw 2.264 2.520 nonbonded pdb=" O2 DC X 27 " pdb=" N2 DG X 59 " model vdw 2.304 2.496 nonbonded pdb=" O LEU D 67 " pdb=" OG1 THR D 70 " model vdw 2.332 2.440 nonbonded pdb=" O ARG C 112 " pdb=" OG1 THR C 116 " model vdw 2.336 2.440 nonbonded pdb=" O TYR C 754 " pdb=" OG SER C 758 " model vdw 2.341 2.440 ... (remaining 189713 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.310 Check model and map are aligned: 0.390 Set scattering table: 0.220 Process input model: 66.600 Find NCS groups from input model: 0.680 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 : 0.003 0.084 24774 Z= 0.177 Angle : 0.595 11.578 33908 Z= 0.362 Chirality : 0.041 0.470 3729 Planarity : 0.005 0.060 4219 Dihedral : 13.750 85.548 9383 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.06 % Allowed : 5.34 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.11), residues: 2837 helix: -2.50 (0.09), residues: 1382 sheet: -1.20 (0.28), residues: 299 loop : -2.38 (0.14), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 652 HIS 0.005 0.000 HIS D 256 PHE 0.014 0.001 PHE B1023 TYR 0.012 0.001 TYR B1111 ARG 0.003 0.000 ARG C 708 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 694 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 VAL cc_start: 0.9226 (t) cc_final: 0.8940 (p) REVERT: B 133 CYS cc_start: 0.8532 (m) cc_final: 0.8209 (m) REVERT: B 152 LEU cc_start: 0.8526 (tp) cc_final: 0.8224 (mt) REVERT: B 335 ILE cc_start: 0.9066 (mt) cc_final: 0.8791 (mt) REVERT: B 348 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7217 (mt-10) REVERT: B 518 MET cc_start: 0.8818 (mmm) cc_final: 0.8403 (mmp) REVERT: B 595 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8115 (pt0) REVERT: B 797 GLU cc_start: 0.8771 (tt0) cc_final: 0.8456 (tm-30) REVERT: B 798 ASP cc_start: 0.7880 (m-30) cc_final: 0.6680 (m-30) REVERT: B 804 VAL cc_start: 0.9106 (t) cc_final: 0.8879 (p) REVERT: B 833 VAL cc_start: 0.8706 (t) cc_final: 0.8494 (t) REVERT: B 1066 ILE cc_start: 0.9334 (mt) cc_final: 0.8434 (mt) REVERT: B 1078 LEU cc_start: 0.8187 (tt) cc_final: 0.7925 (mt) REVERT: B 1111 TYR cc_start: 0.7012 (OUTLIER) cc_final: 0.6037 (t80) REVERT: B 1114 TYR cc_start: 0.8663 (m-10) cc_final: 0.8384 (m-10) REVERT: C 12 VAL cc_start: 0.9109 (t) cc_final: 0.8856 (t) REVERT: C 37 VAL cc_start: 0.7673 (m) cc_final: 0.7427 (p) REVERT: C 69 ILE cc_start: 0.9099 (mm) cc_final: 0.8811 (mt) REVERT: C 91 MET cc_start: 0.8438 (mtm) cc_final: 0.8114 (ttp) REVERT: C 103 LEU cc_start: 0.8895 (mt) cc_final: 0.8424 (tt) REVERT: C 385 GLU cc_start: 0.8458 (tt0) cc_final: 0.7997 (tt0) REVERT: C 465 PHE cc_start: 0.8098 (m-80) cc_final: 0.7868 (m-80) REVERT: C 492 TYR cc_start: 0.7657 (m-80) cc_final: 0.6891 (m-80) REVERT: C 550 TYR cc_start: 0.7484 (t80) cc_final: 0.6527 (t80) REVERT: C 571 LEU cc_start: 0.8955 (mt) cc_final: 0.8731 (mm) REVERT: C 676 CYS cc_start: 0.8160 (m) cc_final: 0.7832 (m) REVERT: C 685 TYR cc_start: 0.8182 (t80) cc_final: 0.7306 (t80) REVERT: C 714 TYR cc_start: 0.8815 (t80) cc_final: 0.8111 (t80) REVERT: C 728 TYR cc_start: 0.7963 (t80) cc_final: 0.6533 (t80) REVERT: C 730 SER cc_start: 0.9204 (t) cc_final: 0.8669 (t) REVERT: C 861 ASP cc_start: 0.8116 (p0) cc_final: 0.7429 (p0) REVERT: D 273 MET cc_start: 0.7489 (mtm) cc_final: 0.7169 (mtt) REVERT: D 407 MET cc_start: 0.8926 (ttp) cc_final: 0.8698 (tmm) REVERT: D 444 LEU cc_start: 0.8735 (mt) cc_final: 0.8531 (tp) REVERT: D 484 ILE cc_start: 0.8703 (mm) cc_final: 0.7982 (tp) REVERT: D 537 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.7958 (p) REVERT: D 600 LEU cc_start: 0.8546 (mt) cc_final: 0.8199 (mp) outliers start: 74 outliers final: 12 residues processed: 750 average time/residue: 0.4006 time to fit residues: 448.7774 Evaluate side-chains 354 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 340 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 244 optimal weight: 7.9990 chunk 219 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 226 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 137 optimal weight: 0.0670 chunk 168 optimal weight: 10.0000 chunk 262 optimal weight: 30.0000 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN B 134 GLN B 181 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 ASN B 458 ASN B 463 GLN B 515 GLN B 531 GLN B 566 GLN B 594 GLN B 610 ASN B 650 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 GLN B 834 HIS B 848 GLN ** B 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 944 GLN B 956 HIS B1084 ASN B1095 GLN B1133 HIS B1134 HIS C 6 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN C 321 GLN C 336 HIS C 423 GLN C 510 ASN C 570 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 GLN C 749 GLN C 759 HIS C 792 GLN C 822 GLN C 881 ASN C 883 GLN C 920 GLN C 925 GLN C 979 GLN C1091 GLN D 128 HIS ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 24774 Z= 0.276 Angle : 0.628 9.090 33908 Z= 0.320 Chirality : 0.040 0.177 3729 Planarity : 0.005 0.055 4219 Dihedral : 14.583 88.505 3843 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.04 % Allowed : 2.98 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.14), residues: 2837 helix: -0.03 (0.13), residues: 1421 sheet: -0.62 (0.29), residues: 291 loop : -1.84 (0.16), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 149 HIS 0.010 0.001 HIS B 956 PHE 0.025 0.002 PHE D 386 TYR 0.025 0.002 TYR D 108 ARG 0.021 0.001 ARG B 728 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 380 time to evaluate : 2.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 VAL cc_start: 0.9188 (t) cc_final: 0.8939 (p) REVERT: B 518 MET cc_start: 0.8718 (mmm) cc_final: 0.8348 (mmp) REVERT: B 599 LEU cc_start: 0.9561 (mp) cc_final: 0.9315 (mt) REVERT: B 661 LEU cc_start: 0.9590 (mt) cc_final: 0.9374 (mt) REVERT: B 731 SER cc_start: 0.8169 (t) cc_final: 0.7939 (m) REVERT: B 797 GLU cc_start: 0.8892 (tt0) cc_final: 0.8444 (tm-30) REVERT: B 798 ASP cc_start: 0.8141 (m-30) cc_final: 0.7815 (m-30) REVERT: B 1061 MET cc_start: 0.4610 (mtp) cc_final: 0.4146 (mmp) REVERT: B 1078 LEU cc_start: 0.8272 (tt) cc_final: 0.8030 (mt) REVERT: B 1114 TYR cc_start: 0.8767 (m-10) cc_final: 0.8493 (m-10) REVERT: B 1170 GLU cc_start: 0.8511 (tp30) cc_final: 0.8281 (pt0) REVERT: C 34 MET cc_start: 0.8575 (mmt) cc_final: 0.8280 (mmm) REVERT: C 103 LEU cc_start: 0.9035 (mt) cc_final: 0.8781 (mt) REVERT: C 115 LEU cc_start: 0.9234 (mp) cc_final: 0.8858 (pp) REVERT: C 465 PHE cc_start: 0.8409 (m-80) cc_final: 0.8135 (m-80) REVERT: C 492 TYR cc_start: 0.7447 (m-80) cc_final: 0.7067 (m-10) REVERT: C 550 TYR cc_start: 0.7261 (t80) cc_final: 0.5520 (t80) REVERT: C 571 LEU cc_start: 0.9249 (mt) cc_final: 0.8844 (mm) REVERT: C 714 TYR cc_start: 0.8774 (t80) cc_final: 0.8049 (t80) REVERT: C 790 ASP cc_start: 0.7786 (t0) cc_final: 0.7296 (t0) REVERT: C 861 ASP cc_start: 0.8018 (p0) cc_final: 0.7706 (p0) REVERT: C 1003 ASP cc_start: 0.7299 (t0) cc_final: 0.6867 (t0) REVERT: D 275 ASP cc_start: 0.8433 (p0) cc_final: 0.8123 (p0) REVERT: D 393 ILE cc_start: 0.8016 (pt) cc_final: 0.7718 (pt) outliers start: 1 outliers final: 0 residues processed: 381 average time/residue: 0.3688 time to fit residues: 217.6674 Evaluate side-chains 238 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 2.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 145 optimal weight: 8.9990 chunk 81 optimal weight: 30.0000 chunk 218 optimal weight: 4.9990 chunk 178 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 262 optimal weight: 5.9990 chunk 284 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 260 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 210 optimal weight: 9.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN B 222 HIS ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN B 278 ASN ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 ASN ** B 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 956 HIS ** B1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 HIS C 380 HIS C 423 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 793 ASN C 881 ASN C 920 GLN ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 ASN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24774 Z= 0.235 Angle : 0.570 8.085 33908 Z= 0.291 Chirality : 0.039 0.189 3729 Planarity : 0.004 0.042 4219 Dihedral : 14.699 87.777 3843 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: -0.30 (0.15), residues: 2837 helix: 0.86 (0.14), residues: 1421 sheet: -0.32 (0.29), residues: 293 loop : -1.53 (0.17), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 652 HIS 0.008 0.001 HIS D 548 PHE 0.023 0.001 PHE B 756 TYR 0.021 0.001 TYR B 97 ARG 0.032 0.001 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 2.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 VAL cc_start: 0.9171 (t) cc_final: 0.8946 (p) REVERT: B 499 MET cc_start: 0.8105 (tpp) cc_final: 0.7466 (tpt) REVERT: B 518 MET cc_start: 0.8822 (mmm) cc_final: 0.8425 (mmp) REVERT: B 520 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8125 (tm-30) REVERT: B 731 SER cc_start: 0.8377 (t) cc_final: 0.8108 (m) REVERT: B 797 GLU cc_start: 0.9002 (tt0) cc_final: 0.8513 (tm-30) REVERT: B 798 ASP cc_start: 0.8146 (m-30) cc_final: 0.7842 (m-30) REVERT: B 902 ARG cc_start: 0.8275 (ptm-80) cc_final: 0.8052 (ptm-80) REVERT: B 1078 LEU cc_start: 0.8236 (tt) cc_final: 0.8003 (mt) REVERT: B 1112 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8265 (tm-30) REVERT: B 1114 TYR cc_start: 0.8832 (m-10) cc_final: 0.8547 (m-10) REVERT: B 1170 GLU cc_start: 0.8492 (tp30) cc_final: 0.8264 (pt0) REVERT: C 103 LEU cc_start: 0.9093 (mt) cc_final: 0.8753 (mt) REVERT: C 115 LEU cc_start: 0.9260 (mp) cc_final: 0.8873 (pp) REVERT: C 389 LEU cc_start: 0.8817 (tp) cc_final: 0.8511 (tp) REVERT: C 465 PHE cc_start: 0.8487 (m-80) cc_final: 0.8170 (m-80) REVERT: C 571 LEU cc_start: 0.9293 (mt) cc_final: 0.8903 (mm) REVERT: C 714 TYR cc_start: 0.8748 (t80) cc_final: 0.7937 (t80) REVERT: C 790 ASP cc_start: 0.7757 (t0) cc_final: 0.7454 (t0) REVERT: C 861 ASP cc_start: 0.8051 (p0) cc_final: 0.7786 (p0) REVERT: C 1057 MET cc_start: 0.7216 (mmm) cc_final: 0.6993 (mmm) REVERT: C 1102 MET cc_start: 0.9071 (ttm) cc_final: 0.8822 (tmm) REVERT: D 393 ILE cc_start: 0.8089 (pt) cc_final: 0.7778 (pt) REVERT: D 484 ILE cc_start: 0.8524 (mm) cc_final: 0.7812 (tp) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.3582 time to fit residues: 184.9145 Evaluate side-chains 231 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 259 optimal weight: 7.9990 chunk 197 optimal weight: 0.8980 chunk 136 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 176 optimal weight: 9.9990 chunk 263 optimal weight: 20.0000 chunk 279 optimal weight: 20.0000 chunk 137 optimal weight: 5.9990 chunk 250 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 GLN B 956 HIS ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1133 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 724 GLN C 881 ASN C 920 GLN D 152 ASN ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 24774 Z= 0.292 Angle : 0.619 10.368 33908 Z= 0.313 Chirality : 0.040 0.160 3729 Planarity : 0.004 0.049 4219 Dihedral : 14.945 89.834 3843 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.12 (0.16), residues: 2837 helix: 1.17 (0.14), residues: 1419 sheet: -0.14 (0.30), residues: 289 loop : -1.28 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 652 HIS 0.008 0.001 HIS D 548 PHE 0.025 0.002 PHE D 386 TYR 0.015 0.002 TYR C 714 ARG 0.012 0.001 ARG C 433 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 499 MET cc_start: 0.8463 (tpp) cc_final: 0.7823 (tpt) REVERT: B 525 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8511 (tp-100) REVERT: B 687 ILE cc_start: 0.9268 (mt) cc_final: 0.8919 (mt) REVERT: B 797 GLU cc_start: 0.9128 (tt0) cc_final: 0.8558 (tm-30) REVERT: B 798 ASP cc_start: 0.8403 (m-30) cc_final: 0.8147 (m-30) REVERT: B 1078 LEU cc_start: 0.8340 (tt) cc_final: 0.8038 (mt) REVERT: B 1112 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8352 (tm-30) REVERT: B 1114 TYR cc_start: 0.8910 (m-10) cc_final: 0.8605 (m-10) REVERT: B 1135 PHE cc_start: 0.7858 (t80) cc_final: 0.7601 (t80) REVERT: B 1170 GLU cc_start: 0.8513 (tp30) cc_final: 0.8245 (pt0) REVERT: C 91 MET cc_start: 0.8426 (mtm) cc_final: 0.8144 (ttp) REVERT: C 134 LEU cc_start: 0.9325 (mm) cc_final: 0.9046 (mm) REVERT: C 230 LEU cc_start: 0.9133 (mt) cc_final: 0.8759 (mt) REVERT: C 385 GLU cc_start: 0.8725 (tt0) cc_final: 0.8477 (tt0) REVERT: C 685 TYR cc_start: 0.8101 (t80) cc_final: 0.7880 (t80) REVERT: C 714 TYR cc_start: 0.8791 (t80) cc_final: 0.7934 (t80) REVERT: C 790 ASP cc_start: 0.8110 (t0) cc_final: 0.7854 (t0) REVERT: C 861 ASP cc_start: 0.8108 (p0) cc_final: 0.7811 (p0) REVERT: C 1057 MET cc_start: 0.7127 (mmm) cc_final: 0.6832 (mmm) REVERT: C 1102 MET cc_start: 0.9064 (ttm) cc_final: 0.8830 (tmm) REVERT: D 393 ILE cc_start: 0.8059 (pt) cc_final: 0.7788 (pt) REVERT: D 484 ILE cc_start: 0.8461 (mm) cc_final: 0.7875 (tp) REVERT: D 545 GLU cc_start: 0.7872 (tt0) cc_final: 0.7410 (mp0) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.3193 time to fit residues: 146.4683 Evaluate side-chains 206 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 232 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 115 optimal weight: 20.0000 chunk 238 optimal weight: 20.0000 chunk 193 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 142 optimal weight: 2.9990 chunk 250 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 HIS B 956 HIS ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN C 510 ASN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24774 Z= 0.252 Angle : 0.593 9.891 33908 Z= 0.298 Chirality : 0.040 0.226 3729 Planarity : 0.004 0.044 4219 Dihedral : 15.100 89.236 3843 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.16), residues: 2837 helix: 1.35 (0.14), residues: 1419 sheet: -0.05 (0.30), residues: 289 loop : -1.17 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 652 HIS 0.009 0.001 HIS D 548 PHE 0.025 0.001 PHE D 386 TYR 0.027 0.002 TYR C 550 ARG 0.005 0.000 ARG C 360 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 2.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 499 MET cc_start: 0.8565 (tpp) cc_final: 0.7763 (tpt) REVERT: B 520 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8094 (tm-30) REVERT: B 525 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8312 (tp-100) REVERT: B 595 GLU cc_start: 0.8195 (pt0) cc_final: 0.7667 (pt0) REVERT: B 727 MET cc_start: 0.8553 (mtt) cc_final: 0.8231 (mtt) REVERT: B 797 GLU cc_start: 0.9169 (tt0) cc_final: 0.8517 (tm-30) REVERT: B 798 ASP cc_start: 0.8412 (m-30) cc_final: 0.8052 (m-30) REVERT: B 1078 LEU cc_start: 0.8260 (tt) cc_final: 0.7975 (mt) REVERT: B 1112 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8344 (tm-30) REVERT: B 1114 TYR cc_start: 0.8949 (m-10) cc_final: 0.8593 (m-10) REVERT: B 1170 GLU cc_start: 0.8539 (tp30) cc_final: 0.8232 (pt0) REVERT: C 13 LEU cc_start: 0.8770 (mm) cc_final: 0.8266 (mm) REVERT: C 91 MET cc_start: 0.8454 (mtm) cc_final: 0.8039 (ttp) REVERT: C 230 LEU cc_start: 0.9076 (mt) cc_final: 0.8726 (mt) REVERT: C 338 ILE cc_start: 0.9487 (mm) cc_final: 0.9225 (tp) REVERT: C 685 TYR cc_start: 0.8308 (t80) cc_final: 0.8037 (t80) REVERT: C 714 TYR cc_start: 0.8708 (t80) cc_final: 0.7772 (t80) REVERT: C 861 ASP cc_start: 0.8158 (p0) cc_final: 0.7889 (p0) REVERT: D 100 MET cc_start: 0.8948 (mpp) cc_final: 0.8637 (mpp) REVERT: D 324 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8086 (pp20) REVERT: D 393 ILE cc_start: 0.8079 (pt) cc_final: 0.7782 (pt) REVERT: D 484 ILE cc_start: 0.8410 (mm) cc_final: 0.7971 (tp) REVERT: D 545 GLU cc_start: 0.7967 (tt0) cc_final: 0.7397 (pm20) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.3306 time to fit residues: 146.8953 Evaluate side-chains 204 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 93 optimal weight: 9.9990 chunk 251 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 279 optimal weight: 9.9990 chunk 232 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 146 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 956 HIS ** B1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1133 HIS ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 24774 Z= 0.271 Angle : 0.612 10.231 33908 Z= 0.309 Chirality : 0.040 0.217 3729 Planarity : 0.004 0.044 4219 Dihedral : 15.249 88.978 3843 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.16), residues: 2837 helix: 1.40 (0.14), residues: 1420 sheet: -0.06 (0.30), residues: 296 loop : -1.11 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 993 HIS 0.007 0.001 HIS B 956 PHE 0.024 0.002 PHE B 645 TYR 0.016 0.002 TYR C 190 ARG 0.007 0.001 ARG C 384 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 2.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 499 MET cc_start: 0.8475 (tpp) cc_final: 0.8235 (tpp) REVERT: B 525 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8213 (tp-100) REVERT: B 595 GLU cc_start: 0.8176 (pt0) cc_final: 0.7765 (pt0) REVERT: B 797 GLU cc_start: 0.9174 (tt0) cc_final: 0.8459 (tm-30) REVERT: B 1112 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8429 (tm-30) REVERT: B 1114 TYR cc_start: 0.8959 (m-10) cc_final: 0.8632 (m-10) REVERT: C 13 LEU cc_start: 0.8663 (mm) cc_final: 0.8160 (mm) REVERT: C 91 MET cc_start: 0.8506 (mtm) cc_final: 0.8078 (ttp) REVERT: C 230 LEU cc_start: 0.9146 (mt) cc_final: 0.8819 (mt) REVERT: C 685 TYR cc_start: 0.8285 (t80) cc_final: 0.7938 (t80) REVERT: C 714 TYR cc_start: 0.8710 (t80) cc_final: 0.7785 (t80) REVERT: C 785 THR cc_start: 0.8625 (p) cc_final: 0.8352 (p) REVERT: D 100 MET cc_start: 0.8910 (mpp) cc_final: 0.8573 (mpp) REVERT: D 324 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8124 (pp20) REVERT: D 393 ILE cc_start: 0.8019 (pt) cc_final: 0.7783 (pt) REVERT: D 484 ILE cc_start: 0.8388 (mm) cc_final: 0.7990 (tp) REVERT: D 545 GLU cc_start: 0.7949 (tt0) cc_final: 0.7419 (pm20) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.3341 time to fit residues: 141.5107 Evaluate side-chains 197 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 269 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 159 optimal weight: 0.9980 chunk 204 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 156 optimal weight: 20.0000 chunk 278 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN B 224 GLN ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 956 HIS ** B1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 699 GLN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24774 Z= 0.181 Angle : 0.563 10.715 33908 Z= 0.282 Chirality : 0.039 0.240 3729 Planarity : 0.004 0.043 4219 Dihedral : 15.256 88.930 3843 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.59 (0.16), residues: 2837 helix: 1.55 (0.14), residues: 1422 sheet: 0.09 (0.31), residues: 281 loop : -1.03 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 248 HIS 0.009 0.001 HIS B 956 PHE 0.023 0.001 PHE C 68 TYR 0.030 0.001 TYR C 550 ARG 0.004 0.000 ARG C 384 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 453 MET cc_start: 0.8172 (ptm) cc_final: 0.7570 (ttp) REVERT: B 499 MET cc_start: 0.8435 (tpp) cc_final: 0.8047 (tpt) REVERT: B 503 LEU cc_start: 0.8781 (tt) cc_final: 0.8131 (pp) REVERT: B 525 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8084 (tp-100) REVERT: B 595 GLU cc_start: 0.8112 (pt0) cc_final: 0.7862 (pt0) REVERT: B 727 MET cc_start: 0.8595 (mtt) cc_final: 0.8305 (mtt) REVERT: B 797 GLU cc_start: 0.9129 (tt0) cc_final: 0.8478 (tm-30) REVERT: B 798 ASP cc_start: 0.8443 (m-30) cc_final: 0.8018 (m-30) REVERT: B 1066 ILE cc_start: 0.9277 (mt) cc_final: 0.7967 (mt) REVERT: B 1112 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8454 (tm-30) REVERT: B 1114 TYR cc_start: 0.8889 (m-10) cc_final: 0.8561 (m-10) REVERT: C 91 MET cc_start: 0.8478 (mtm) cc_final: 0.8069 (ttp) REVERT: C 230 LEU cc_start: 0.9104 (mt) cc_final: 0.8777 (mt) REVERT: C 548 LEU cc_start: 0.8960 (tt) cc_final: 0.8733 (tt) REVERT: C 685 TYR cc_start: 0.8229 (t80) cc_final: 0.7887 (t80) REVERT: C 714 TYR cc_start: 0.8645 (t80) cc_final: 0.7802 (t80) REVERT: C 785 THR cc_start: 0.8573 (p) cc_final: 0.8293 (p) REVERT: C 861 ASP cc_start: 0.8163 (p0) cc_final: 0.7905 (p0) REVERT: D 100 MET cc_start: 0.8851 (mpp) cc_final: 0.8574 (mpp) REVERT: D 484 ILE cc_start: 0.8479 (mm) cc_final: 0.8173 (tp) REVERT: D 545 GLU cc_start: 0.7916 (tt0) cc_final: 0.7446 (pm20) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.3330 time to fit residues: 154.3184 Evaluate side-chains 201 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 172 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 53 optimal weight: 0.0060 chunk 177 optimal weight: 2.9990 chunk 189 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 GLN ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 956 HIS ** B1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1133 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24774 Z= 0.175 Angle : 0.558 9.800 33908 Z= 0.281 Chirality : 0.039 0.213 3729 Planarity : 0.004 0.099 4219 Dihedral : 15.220 89.863 3843 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.04 % Allowed : 0.70 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.67 (0.16), residues: 2837 helix: 1.62 (0.14), residues: 1423 sheet: -0.00 (0.30), residues: 282 loop : -0.95 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP B 236 HIS 0.009 0.001 HIS B 956 PHE 0.026 0.001 PHE C 125 TYR 0.014 0.001 TYR B1111 ARG 0.007 0.000 ARG D 504 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 273 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 499 MET cc_start: 0.8388 (tpp) cc_final: 0.7919 (tpt) REVERT: B 503 LEU cc_start: 0.8787 (tt) cc_final: 0.8132 (pp) REVERT: B 525 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8059 (tp-100) REVERT: B 595 GLU cc_start: 0.8236 (pt0) cc_final: 0.7780 (pt0) REVERT: B 661 LEU cc_start: 0.9565 (mt) cc_final: 0.9360 (mt) REVERT: B 727 MET cc_start: 0.8597 (mtt) cc_final: 0.8299 (mtt) REVERT: B 797 GLU cc_start: 0.9121 (tt0) cc_final: 0.8474 (tm-30) REVERT: B 798 ASP cc_start: 0.8435 (m-30) cc_final: 0.8083 (m-30) REVERT: B 1112 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8435 (tm-30) REVERT: B 1114 TYR cc_start: 0.8888 (m-10) cc_final: 0.8542 (m-10) REVERT: C 91 MET cc_start: 0.8511 (mtm) cc_final: 0.8104 (ttp) REVERT: C 230 LEU cc_start: 0.9102 (mt) cc_final: 0.8779 (mt) REVERT: C 396 MET cc_start: 0.8420 (tpp) cc_final: 0.8176 (tpp) REVERT: C 548 LEU cc_start: 0.8961 (tt) cc_final: 0.8748 (tt) REVERT: C 685 TYR cc_start: 0.7897 (t80) cc_final: 0.7555 (t80) REVERT: C 712 ASP cc_start: 0.8278 (m-30) cc_final: 0.8042 (m-30) REVERT: C 714 TYR cc_start: 0.8655 (t80) cc_final: 0.7808 (t80) REVERT: C 785 THR cc_start: 0.8557 (p) cc_final: 0.8267 (p) REVERT: C 861 ASP cc_start: 0.8188 (p0) cc_final: 0.7932 (p0) REVERT: D 275 ASP cc_start: 0.8636 (p0) cc_final: 0.8419 (p0) REVERT: D 484 ILE cc_start: 0.8462 (mm) cc_final: 0.8140 (tp) REVERT: D 545 GLU cc_start: 0.7883 (tt0) cc_final: 0.7432 (pm20) outliers start: 1 outliers final: 0 residues processed: 274 average time/residue: 0.3230 time to fit residues: 145.9628 Evaluate side-chains 202 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 253 optimal weight: 20.0000 chunk 266 optimal weight: 9.9990 chunk 243 optimal weight: 7.9990 chunk 259 optimal weight: 30.0000 chunk 156 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 203 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 234 optimal weight: 0.4980 chunk 245 optimal weight: 8.9990 chunk 258 optimal weight: 0.0770 overall best weight: 3.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 956 HIS ** B1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24774 Z= 0.252 Angle : 0.601 9.547 33908 Z= 0.302 Chirality : 0.040 0.215 3729 Planarity : 0.004 0.042 4219 Dihedral : 15.268 88.755 3843 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.61 (0.16), residues: 2837 helix: 1.56 (0.14), residues: 1428 sheet: -0.04 (0.30), residues: 296 loop : -0.98 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B 236 HIS 0.009 0.001 HIS B 956 PHE 0.022 0.001 PHE D 386 TYR 0.026 0.001 TYR C 550 ARG 0.008 0.001 ARG D 325 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 499 MET cc_start: 0.8443 (tpp) cc_final: 0.7962 (tpt) REVERT: B 525 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8089 (tp-100) REVERT: B 595 GLU cc_start: 0.8299 (pt0) cc_final: 0.7804 (pt0) REVERT: B 596 MET cc_start: 0.9014 (mmt) cc_final: 0.8603 (mmp) REVERT: B 661 LEU cc_start: 0.9574 (mt) cc_final: 0.9314 (mt) REVERT: B 727 MET cc_start: 0.8296 (mtt) cc_final: 0.8022 (mtt) REVERT: B 797 GLU cc_start: 0.9165 (tt0) cc_final: 0.8451 (tm-30) REVERT: B 1066 ILE cc_start: 0.9285 (mt) cc_final: 0.7963 (mt) REVERT: B 1112 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8481 (tm-30) REVERT: B 1114 TYR cc_start: 0.8930 (m-10) cc_final: 0.8567 (m-10) REVERT: C 91 MET cc_start: 0.8543 (mtm) cc_final: 0.8179 (ttp) REVERT: C 230 LEU cc_start: 0.9117 (mt) cc_final: 0.8803 (mt) REVERT: C 396 MET cc_start: 0.8418 (tpp) cc_final: 0.8165 (tpp) REVERT: C 548 LEU cc_start: 0.8876 (tt) cc_final: 0.8649 (tt) REVERT: C 685 TYR cc_start: 0.7914 (t80) cc_final: 0.7362 (t80) REVERT: C 712 ASP cc_start: 0.8338 (m-30) cc_final: 0.7965 (m-30) REVERT: C 714 TYR cc_start: 0.8715 (t80) cc_final: 0.7900 (t80) REVERT: C 785 THR cc_start: 0.8617 (p) cc_final: 0.8386 (p) REVERT: D 324 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8174 (pp20) REVERT: D 484 ILE cc_start: 0.8417 (mm) cc_final: 0.8194 (tp) REVERT: D 488 ASP cc_start: 0.8358 (t0) cc_final: 0.8114 (t0) REVERT: D 545 GLU cc_start: 0.7897 (tt0) cc_final: 0.7329 (pm20) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.3135 time to fit residues: 133.0666 Evaluate side-chains 188 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 170 optimal weight: 7.9990 chunk 274 optimal weight: 10.0000 chunk 167 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 190 optimal weight: 0.0270 chunk 287 optimal weight: 10.0000 chunk 264 optimal weight: 9.9990 chunk 229 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN B 689 HIS ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 956 HIS ** B1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 HIS B1133 HIS ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24774 Z= 0.170 Angle : 0.571 9.250 33908 Z= 0.285 Chirality : 0.040 0.239 3729 Planarity : 0.004 0.042 4219 Dihedral : 15.208 89.442 3843 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.73 (0.16), residues: 2837 helix: 1.67 (0.14), residues: 1426 sheet: 0.02 (0.31), residues: 276 loop : -0.93 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 236 HIS 0.009 0.001 HIS B 956 PHE 0.021 0.001 PHE D 386 TYR 0.014 0.001 TYR B1111 ARG 0.009 0.000 ARG B 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 2.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 GLU cc_start: 0.8984 (tt0) cc_final: 0.8762 (tm-30) REVERT: B 453 MET cc_start: 0.8213 (ptm) cc_final: 0.7795 (ttp) REVERT: B 499 MET cc_start: 0.8385 (tpp) cc_final: 0.7871 (tpt) REVERT: B 525 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8069 (tp-100) REVERT: B 661 LEU cc_start: 0.9539 (mt) cc_final: 0.9337 (mt) REVERT: B 727 MET cc_start: 0.8365 (mtt) cc_final: 0.8146 (mtt) REVERT: B 797 GLU cc_start: 0.9107 (tt0) cc_final: 0.8500 (tm-30) REVERT: B 798 ASP cc_start: 0.8421 (m-30) cc_final: 0.8022 (m-30) REVERT: B 1066 ILE cc_start: 0.9273 (mt) cc_final: 0.7874 (mt) REVERT: B 1112 GLN cc_start: 0.8860 (tm-30) cc_final: 0.8538 (tm-30) REVERT: B 1114 TYR cc_start: 0.8843 (m-10) cc_final: 0.8519 (m-10) REVERT: C 91 MET cc_start: 0.8543 (mtm) cc_final: 0.8166 (ttp) REVERT: C 230 LEU cc_start: 0.9142 (mt) cc_final: 0.8789 (mt) REVERT: C 342 ILE cc_start: 0.9521 (tt) cc_final: 0.9307 (tp) REVERT: C 396 MET cc_start: 0.8387 (tpp) cc_final: 0.8129 (tpp) REVERT: C 685 TYR cc_start: 0.7853 (t80) cc_final: 0.7306 (t80) REVERT: C 712 ASP cc_start: 0.8295 (m-30) cc_final: 0.7919 (m-30) REVERT: C 714 TYR cc_start: 0.8637 (t80) cc_final: 0.7906 (t80) REVERT: C 785 THR cc_start: 0.8589 (p) cc_final: 0.8336 (p) REVERT: D 275 ASP cc_start: 0.8490 (p0) cc_final: 0.8286 (p0) REVERT: D 545 GLU cc_start: 0.7878 (tt0) cc_final: 0.7424 (pm20) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.3407 time to fit residues: 145.7788 Evaluate side-chains 195 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 182 optimal weight: 0.0980 chunk 244 optimal weight: 20.0000 chunk 70 optimal weight: 6.9990 chunk 211 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 229 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 235 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 GLN ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 GLN ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 956 HIS ** B1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.073164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.058215 restraints weight = 111367.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.059842 restraints weight = 64025.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.060944 restraints weight = 43280.806| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24774 Z= 0.156 Angle : 0.564 9.095 33908 Z= 0.281 Chirality : 0.039 0.224 3729 Planarity : 0.003 0.043 4219 Dihedral : 15.121 89.772 3843 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.04 % Allowed : 0.33 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.84 (0.16), residues: 2837 helix: 1.75 (0.14), residues: 1431 sheet: 0.07 (0.31), residues: 288 loop : -0.88 (0.19), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 236 HIS 0.009 0.001 HIS B 956 PHE 0.024 0.001 PHE C 68 TYR 0.014 0.001 TYR B1111 ARG 0.008 0.000 ARG B 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4432.26 seconds wall clock time: 81 minutes 4.93 seconds (4864.93 seconds total)