Starting phenix.real_space_refine on Tue Mar 19 09:37:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t2v_10370/03_2024/6t2v_10370.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t2v_10370/03_2024/6t2v_10370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t2v_10370/03_2024/6t2v_10370.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t2v_10370/03_2024/6t2v_10370.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t2v_10370/03_2024/6t2v_10370.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t2v_10370/03_2024/6t2v_10370.pdb" } resolution = 3.8 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= 0.005 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 54 5.49 5 S 101 5.16 5 C 14897 2.51 5 N 4192 2.21 5 O 4582 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 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 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 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 108": "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 TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ARG 392": "NH1" <-> "NH2" Residue "C TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 433": "NH1" <-> "NH2" Residue "C TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 442": "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 ARG 653": "NH1" <-> "NH2" Residue "C ARG 703": "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 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23826 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: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1098 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain breaks: 1 Time building chain proxies: 12.50, per 1000 atoms: 0.52 Number of scatterers: 23826 At special positions: 0 Unit cell: (152.985, 150.815, 131.285, 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 54 15.00 O 4582 8.00 N 4192 7.00 C 14897 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: 9.43 Conformation dependent library (CDL) restraints added in 4.3 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: 124 helices and 16 sheets defined 53.1% alpha, 9.2% beta 18 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 7.59 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: 3.556A pdb=" N GLU B 58 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 59 " --> pdb=" O VAL B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 59' Processing helix chain 'B' and resid 65 through 90 Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.642A 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 128 through 140 Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.622A pdb=" N SER B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 173 removed outlier: 3.820A pdb=" N TYR B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.256A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 3.678A pdb=" N LEU B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 239 removed outlier: 3.559A 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: 3.625A pdb=" N ASN B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.760A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 317 removed outlier: 4.251A pdb=" N GLU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 4.469A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.529A pdb=" N MET B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU B 355 " --> pdb=" O PHE B 351 " (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: 3.756A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.829A 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 Processing helix chain 'B' and resid 560 through 573 Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 590 through 605 removed outlier: 3.953A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.801A pdb=" N LEU B 612 " --> pdb=" O ARG B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 634 Processing helix chain 'B' and resid 634 through 655 removed outlier: 3.613A pdb=" N TRP B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 668 removed outlier: 3.806A pdb=" N MET B 660 " --> pdb=" O GLY B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 677 removed outlier: 3.607A pdb=" N ASN B 673 " --> pdb=" O ASN B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 699 removed outlier: 3.619A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 717 removed outlier: 4.103A pdb=" N LEU B 707 " --> pdb=" O SER B 703 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 807 removed outlier: 3.514A 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: 3.764A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 860 removed outlier: 3.900A pdb=" N LEU B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) 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: 3.880A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1012 removed outlier: 3.707A pdb=" N GLN B1011 " --> pdb=" O SER B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 3.633A pdb=" N THR B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 3.894A 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: 3.800A 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: 3.563A pdb=" N LEU B1167 " --> pdb=" O GLY B1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 4.139A 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 102 removed outlier: 3.741A pdb=" N THR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 108 through 116 Processing helix chain 'C' and resid 122 through 142 Processing helix chain 'C' and resid 142 through 152 removed outlier: 3.898A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 179 Proline residue: C 167 - end of helix Processing helix chain 'C' and resid 189 through 199 Processing helix chain 'C' and resid 220 through 232 removed outlier: 3.568A pdb=" N ALA C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 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 removed outlier: 3.605A pdb=" N VAL C 386 " --> pdb=" O PRO C 382 " (cutoff:3.500A) 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 414 through 428 removed outlier: 3.667A pdb=" N TYR C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) Proline residue: C 420 - end of helix Processing helix chain 'C' and resid 447 through 459 removed outlier: 3.868A pdb=" N ALA C 453 " --> pdb=" O PRO C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 474 Processing helix chain 'C' and resid 476 through 483 removed outlier: 3.593A pdb=" N PHE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.786A pdb=" N GLN C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 removed outlier: 3.575A 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 574 removed outlier: 3.726A pdb=" N MET C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 599 removed outlier: 4.590A pdb=" N CYS C 591 " --> pdb=" O TRP C 587 " (cutoff:3.500A) removed outlier: 4.555A 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: 3.849A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 722 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 removed outlier: 3.546A pdb=" N GLN C 812 " --> pdb=" O PRO C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 843 removed outlier: 3.521A pdb=" N LEU C 837 " --> pdb=" O PRO C 833 " (cutoff:3.500A) removed outlier: 3.833A 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: 3.621A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 904 " --> pdb=" O ARG C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 932 removed outlier: 3.767A pdb=" N GLU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 3.838A 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: 3.575A pdb=" N GLY C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1033 removed outlier: 3.696A pdb=" N SER C1032 " --> pdb=" O ARG C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1049 Processing helix chain 'C' and resid 1060 through 1076 removed outlier: 3.571A pdb=" N ARG C1068 " --> pdb=" O LEU C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1089 through 1094 removed outlier: 4.266A pdb=" N LEU C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1113 Processing helix chain 'C' and resid 1113 through 1119 removed outlier: 3.924A pdb=" N PHE C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE C1119 " --> pdb=" O PRO C1115 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.766A 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: 3.970A 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 removed outlier: 3.547A pdb=" N LEU D 137 " --> pdb=" O ASP D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 164 removed outlier: 3.515A 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: 3.647A pdb=" N ARG D 221 " --> pdb=" O GLY D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 244 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.563A pdb=" N MET D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 286 removed outlier: 3.569A pdb=" N ALA D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 315 removed outlier: 3.739A pdb=" N ASP D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 322 through 334 removed outlier: 3.519A 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: 3.813A pdb=" N GLN D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.537A pdb=" N ALA D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 391 removed outlier: 3.539A 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 Processing helix chain 'D' and resid 450 through 465 Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.534A pdb=" N LEU D 527 " --> pdb=" O PRO D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 572 Processing helix chain 'D' and resid 582 through 592 removed outlier: 3.661A pdb=" N ILE D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 3.749A 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: 6.497A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ALA B 439 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 20 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY B 17 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU B 411 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA B 381 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE B 412 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE B 383 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL B 62 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 5.777A 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: 6.294A 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: 6.591A pdb=" N VAL B 207 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 487 through 490 Processing sheet with id=AA5, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.643A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE B 554 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N VAL B 739 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1155 through 1158 removed outlier: 7.225A pdb=" N TYR B1076 " --> pdb=" O GLY B1137 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ILE B1139 " --> pdb=" O TYR B1076 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU B1078 " --> pdb=" O ILE B1139 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU B1141 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA B1080 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N TYR B1081 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 10.123A pdb=" N ILE B1066 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N MET B1061 " --> pdb=" O PRO B1026 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS B1063 " --> pdb=" O TYR B1024 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR B1024 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N PHE B1065 " --> pdb=" O GLU B1022 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU B1022 " --> pdb=" O PHE B1065 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP B1067 " --> pdb=" O GLU B1020 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 57 " --> pdb=" O TYR B1024 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.370A pdb=" N VAL C 211 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU C 239 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE C 213 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR C 241 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG C 3 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N PHE C 240 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N TYR C 5 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG C 266 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP C 324 " --> pdb=" O ARG C 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 365 through 366 removed outlier: 5.928A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 437 through 439 removed outlier: 3.645A pdb=" N ASN C 660 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS C 673 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N TYR C 728 " --> pdb=" O LYS C 673 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N CYS C 782 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N PHE C 376 " --> pdb=" O CYS C 782 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 442 through 443 removed outlier: 3.723A pdb=" N ARG C 442 " --> pdb=" O ILE C 650 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 939 through 947 removed outlier: 5.653A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 15.752A pdb=" N LEU C 956 " --> pdb=" O TRP C 967 " (cutoff:3.500A) removed outlier: 13.340A pdb=" N TRP C 967 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLN C 958 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU C 965 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1050 through 1051 removed outlier: 3.516A pdb=" N ALA C1056 " --> pdb=" O ASP C1051 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.198A 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: 6.585A pdb=" N ARG D 200 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N SER D 238 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.395A 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: 7.199A pdb=" N ASP D 547 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLN D 439 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE D 552 " --> pdb=" O GLN D 439 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU D 441 " --> pdb=" O ILE D 552 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.459A 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: 4.488A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) 1051 hydrogen bonds defined for protein. 3087 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 10.16 Time building geometry restraints manager: 10.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7590 1.34 - 1.45: 3403 1.45 - 1.57: 13184 1.57 - 1.69: 106 1.69 - 1.81: 169 Bond restraints: 24452 Sorted by residual: bond pdb=" N GLU B1073 " pdb=" CA GLU B1073 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.19e+00 bond pdb=" C PRO C 823 " pdb=" N LEU C 824 " ideal model delta sigma weight residual 1.331 1.353 -0.022 2.07e-02 2.33e+03 1.17e+00 bond pdb=" C ILE C 670 " pdb=" O ILE C 670 " ideal model delta sigma weight residual 1.232 1.240 -0.008 8.90e-03 1.26e+04 8.47e-01 bond pdb=" C SER C 419 " pdb=" N PRO C 420 " ideal model delta sigma weight residual 1.335 1.348 -0.012 1.36e-02 5.41e+03 8.32e-01 bond pdb=" CB PRO C 63 " pdb=" CG PRO C 63 " ideal model delta sigma weight residual 1.492 1.537 -0.045 5.00e-02 4.00e+02 8.22e-01 ... (remaining 24447 not shown) Histogram of bond angle deviations from ideal: 100.17 - 106.92: 1077 106.92 - 113.68: 13129 113.68 - 120.44: 10166 120.44 - 127.20: 8694 127.20 - 133.96: 343 Bond angle restraints: 33409 Sorted by residual: angle pdb=" C PHE B 468 " pdb=" N MET B 469 " pdb=" CA MET B 469 " ideal model delta sigma weight residual 121.54 128.49 -6.95 1.91e+00 2.74e-01 1.33e+01 angle pdb=" N GLY B 898 " pdb=" CA GLY B 898 " pdb=" C GLY B 898 " ideal model delta sigma weight residual 110.87 115.76 -4.89 1.54e+00 4.22e-01 1.01e+01 angle pdb=" N TRP B 878 " pdb=" CA TRP B 878 " pdb=" C TRP B 878 " ideal model delta sigma weight residual 107.88 112.25 -4.37 1.41e+00 5.03e-01 9.59e+00 angle pdb=" C SER C 447 " pdb=" N HIS C 448 " pdb=" CA HIS C 448 " ideal model delta sigma weight residual 119.78 123.18 -3.40 1.24e+00 6.50e-01 7.51e+00 angle pdb=" CA GLY C 938 " pdb=" C GLY C 938 " pdb=" N GLN C 939 " ideal model delta sigma weight residual 114.98 117.50 -2.52 1.14e+00 7.69e-01 4.90e+00 ... (remaining 33404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 13284 15.26 - 30.53: 832 30.53 - 45.79: 325 45.79 - 61.06: 164 61.06 - 76.32: 10 Dihedral angle restraints: 14615 sinusoidal: 6326 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 -160.86 -19.14 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA GLY C 657 " pdb=" C GLY C 657 " pdb=" N PRO C 658 " pdb=" CA PRO C 658 " ideal model delta harmonic sigma weight residual 180.00 163.49 16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA THR B 304 " pdb=" C THR B 304 " pdb=" N PRO B 305 " pdb=" CA PRO B 305 " ideal model delta harmonic sigma weight residual 180.00 164.26 15.74 0 5.00e+00 4.00e-02 9.90e+00 ... (remaining 14612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2423 0.026 - 0.052: 828 0.052 - 0.078: 240 0.078 - 0.104: 134 0.104 - 0.131: 48 Chirality restraints: 3673 Sorted by residual: chirality pdb=" CA ILE D 233 " pdb=" N ILE D 233 " pdb=" C ILE D 233 " pdb=" CB ILE D 233 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA ILE C 661 " pdb=" N ILE C 661 " pdb=" C ILE C 661 " pdb=" CB ILE C 661 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA VAL D 337 " pdb=" N VAL D 337 " pdb=" C VAL D 337 " pdb=" CB VAL D 337 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 3670 not shown) Planarity restraints: 4205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 992 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C GLU B 992 " -0.057 2.00e-02 2.50e+03 pdb=" O GLU B 992 " 0.021 2.00e-02 2.50e+03 pdb=" N TRP B 993 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " 0.049 5.00e-02 4.00e+02 7.36e-02 8.66e+00 pdb=" N PRO C 658 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 469 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C ASP C 469 " -0.048 2.00e-02 2.50e+03 pdb=" O ASP C 469 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL C 470 " 0.016 2.00e-02 2.50e+03 ... (remaining 4202 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2695 2.75 - 3.29: 21379 3.29 - 3.83: 39009 3.83 - 4.36: 44859 4.36 - 4.90: 77256 Nonbonded interactions: 185198 Sorted by model distance: nonbonded pdb=" OD1 ASN B 759 " pdb=" NH2 ARG B 822 " model vdw 2.213 2.520 nonbonded pdb=" OG SER D 303 " pdb=" O GLY D 307 " model vdw 2.285 2.440 nonbonded pdb=" NH2 ARG B 254 " pdb=" O3' DG X 61 " model vdw 2.292 2.520 nonbonded pdb=" O LEU C 115 " pdb=" OG SER C 119 " model vdw 2.295 2.440 nonbonded pdb=" OH TYR B 394 " pdb=" OE1 GLU B 436 " model vdw 2.304 2.440 ... (remaining 185193 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: 0.650 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 3.840 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 69.580 Find NCS groups from input model: 0.860 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24452 Z= 0.106 Angle : 0.453 6.953 33409 Z= 0.287 Chirality : 0.034 0.131 3673 Planarity : 0.005 0.074 4205 Dihedral : 13.085 76.320 9243 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.01 % Favored : 97.96 % Rotamer: Outliers : 3.02 % Allowed : 5.18 % Favored : 91.80 % 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: -3.62 (0.11), residues: 2837 helix: -2.53 (0.09), residues: 1409 sheet: -0.87 (0.29), residues: 276 loop : -2.44 (0.14), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 652 HIS 0.002 0.000 HIS C 377 PHE 0.007 0.000 PHE B1023 TYR 0.007 0.001 TYR B1093 ARG 0.003 0.000 ARG B 800 *********************** 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 514 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 441 time to evaluate : 2.684 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: B 166 ASP cc_start: 0.9158 (m-30) cc_final: 0.8830 (m-30) REVERT: B 269 ILE cc_start: 0.6919 (OUTLIER) cc_final: 0.5762 (mm) REVERT: B 354 MET cc_start: 0.7717 (mtt) cc_final: 0.7479 (mtm) REVERT: B 431 MET cc_start: 0.9115 (mtm) cc_final: 0.8620 (mtp) REVERT: B 499 MET cc_start: 0.8110 (ttp) cc_final: 0.7780 (tpp) REVERT: B 501 MET cc_start: 0.9116 (mtm) cc_final: 0.8339 (mpp) REVERT: B 518 MET cc_start: 0.7577 (mmm) cc_final: 0.6306 (mmm) REVERT: B 541 MET cc_start: 0.8598 (mtp) cc_final: 0.7617 (tpp) REVERT: B 588 PHE cc_start: 0.8255 (m-80) cc_final: 0.7894 (m-80) REVERT: B 594 GLN cc_start: 0.8864 (tp-100) cc_final: 0.8458 (tp-100) REVERT: B 658 MET cc_start: 0.8796 (tpp) cc_final: 0.8531 (tpt) REVERT: B 711 LEU cc_start: 0.9635 (tp) cc_final: 0.9386 (tp) REVERT: B 753 TRP cc_start: 0.9178 (OUTLIER) cc_final: 0.7614 (t60) REVERT: B 964 PHE cc_start: 0.8239 (m-80) cc_final: 0.7892 (m-10) REVERT: B 1021 MET cc_start: 0.9165 (ttp) cc_final: 0.8732 (ppp) REVERT: C 50 LEU cc_start: 0.9252 (mt) cc_final: 0.9011 (tt) REVERT: C 91 MET cc_start: 0.8431 (mtm) cc_final: 0.8100 (mtm) REVERT: C 133 ASP cc_start: 0.8831 (t0) cc_final: 0.8506 (m-30) REVERT: C 165 GLN cc_start: 0.9140 (mt0) cc_final: 0.8781 (mt0) REVERT: C 234 ILE cc_start: 0.7021 (OUTLIER) cc_final: 0.6812 (mm) REVERT: C 408 ILE cc_start: 0.9364 (mt) cc_final: 0.8940 (pt) REVERT: C 465 PHE cc_start: 0.8373 (m-80) cc_final: 0.7752 (m-80) REVERT: C 471 LEU cc_start: 0.8936 (mt) cc_final: 0.8544 (pp) REVERT: C 906 ASP cc_start: 0.8350 (m-30) cc_final: 0.8019 (t0) REVERT: C 980 LEU cc_start: 0.8905 (tp) cc_final: 0.8663 (tp) REVERT: D 25 LEU cc_start: 0.9307 (mt) cc_final: 0.8994 (pp) REVERT: D 100 MET cc_start: 0.9257 (mtm) cc_final: 0.8885 (mpp) REVERT: D 108 TYR cc_start: 0.6563 (OUTLIER) cc_final: 0.5915 (p90) REVERT: D 201 LEU cc_start: 0.9360 (mt) cc_final: 0.9097 (tp) REVERT: D 212 LEU cc_start: 0.9492 (tp) cc_final: 0.8917 (tp) REVERT: D 273 MET cc_start: 0.8275 (mtm) cc_final: 0.8005 (ttt) REVERT: D 280 SER cc_start: 0.7789 (p) cc_final: 0.6701 (p) REVERT: D 282 LEU cc_start: 0.9357 (tp) cc_final: 0.9063 (pp) outliers start: 73 outliers final: 13 residues processed: 508 average time/residue: 0.3625 time to fit residues: 281.3888 Evaluate side-chains 257 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 240 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 493 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 30.0000 chunk 218 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 137 optimal weight: 0.8980 chunk 168 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 overall best weight: 7.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN B 150 GLN B 181 GLN B 222 HIS ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 ASN B 455 ASN B 458 ASN B 463 GLN B 562 GLN B 566 GLN B 594 GLN B 610 ASN B 650 GLN B 713 GLN B 765 GLN B 848 GLN B 944 GLN B 971 ASN ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 HIS ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1133 HIS B1134 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN C 390 HIS C 510 ASN C 570 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 GLN C 660 ASN ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 749 GLN ** C 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 HIS C 822 GLN C 843 HIS C 883 GLN C 925 GLN C 951 GLN C1091 GLN C1108 GLN D 22 GLN D 89 GLN D 115 ASN D 152 ASN D 251 GLN D 469 HIS ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 24452 Z= 0.376 Angle : 0.754 11.544 33409 Z= 0.381 Chirality : 0.043 0.315 3673 Planarity : 0.006 0.066 4205 Dihedral : 13.673 83.360 3732 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.27 % Allowed : 11.64 % Favored : 85.09 % 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: -1.14 (0.14), residues: 2837 helix: 0.10 (0.13), residues: 1429 sheet: -0.57 (0.29), residues: 280 loop : -1.88 (0.16), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 652 HIS 0.011 0.002 HIS C 233 PHE 0.022 0.002 PHE C 526 TYR 0.021 0.002 TYR B1111 ARG 0.028 0.001 ARG B 974 *********************** 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 273 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 194 time to evaluate : 2.759 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: B 264 LYS cc_start: 0.9272 (pttm) cc_final: 0.9036 (pttm) REVERT: B 354 MET cc_start: 0.8052 (mtt) cc_final: 0.7681 (mtm) REVERT: B 431 MET cc_start: 0.9071 (mtm) cc_final: 0.8735 (mtp) REVERT: B 501 MET cc_start: 0.9490 (mtm) cc_final: 0.8696 (mtm) REVERT: B 518 MET cc_start: 0.8066 (mmm) cc_final: 0.7758 (mmm) REVERT: B 541 MET cc_start: 0.8598 (mtp) cc_final: 0.7572 (tpp) REVERT: B 559 ARG cc_start: 0.8514 (ttp-170) cc_final: 0.8170 (ttt90) REVERT: B 594 GLN cc_start: 0.9027 (tp40) cc_final: 0.8433 (tp-100) REVERT: B 658 MET cc_start: 0.9101 (tpp) cc_final: 0.8846 (mmm) REVERT: B 753 TRP cc_start: 0.9278 (OUTLIER) cc_final: 0.7723 (t60) REVERT: B 1111 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.8387 (p90) REVERT: C 1 MET cc_start: 0.7554 (tpp) cc_final: 0.7318 (tmm) REVERT: C 17 MET cc_start: 0.9311 (ptm) cc_final: 0.9050 (ptp) REVERT: C 50 LEU cc_start: 0.9317 (mt) cc_final: 0.9062 (tt) REVERT: C 89 GLN cc_start: 0.8517 (pm20) cc_final: 0.8143 (pm20) REVERT: C 408 ILE cc_start: 0.9588 (mt) cc_final: 0.9259 (pt) REVERT: C 665 MET cc_start: 0.7679 (mtp) cc_final: 0.7210 (mtp) REVERT: C 667 MET cc_start: 0.6094 (ttm) cc_final: 0.5017 (ttm) REVERT: C 1102 MET cc_start: 0.9442 (ttt) cc_final: 0.9178 (ttp) REVERT: D 25 LEU cc_start: 0.9420 (mt) cc_final: 0.9203 (tt) REVERT: D 108 TYR cc_start: 0.6677 (OUTLIER) cc_final: 0.6125 (p90) REVERT: D 112 MET cc_start: 0.8769 (tpp) cc_final: 0.8523 (ttm) REVERT: D 269 ASP cc_start: 0.8814 (t0) cc_final: 0.8589 (p0) REVERT: D 273 MET cc_start: 0.8259 (mtm) cc_final: 0.8013 (ttp) REVERT: D 471 HIS cc_start: 0.8394 (m90) cc_final: 0.7955 (m-70) REVERT: D 536 MET cc_start: 0.6018 (tpt) cc_final: 0.5315 (tpt) outliers start: 79 outliers final: 47 residues processed: 261 average time/residue: 0.3322 time to fit residues: 140.9070 Evaluate side-chains 212 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 162 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 954 PHE Chi-restraints excluded: chain B residue 971 ASN Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 217 optimal weight: 7.9990 chunk 178 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 262 optimal weight: 40.0000 chunk 283 optimal weight: 20.0000 chunk 233 optimal weight: 8.9990 chunk 259 optimal weight: 6.9990 chunk 89 optimal weight: 30.0000 chunk 210 optimal weight: 5.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 689 HIS ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1112 GLN C 137 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN ** C 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 881 ASN C 920 GLN D 115 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24452 Z= 0.262 Angle : 0.609 10.746 33409 Z= 0.305 Chirality : 0.039 0.220 3673 Planarity : 0.004 0.070 4205 Dihedral : 13.760 85.493 3721 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.19 % Allowed : 11.64 % Favored : 85.18 % 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 (0.15), residues: 2837 helix: 0.89 (0.14), residues: 1444 sheet: -0.39 (0.29), residues: 275 loop : -1.67 (0.17), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 272 HIS 0.007 0.001 HIS D 289 PHE 0.015 0.001 PHE B 351 TYR 0.015 0.001 TYR B 394 ARG 0.012 0.000 ARG B 974 *********************** 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 246 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 169 time to evaluate : 2.459 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: B 123 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8744 (pm20) REVERT: B 155 ASP cc_start: 0.8150 (p0) cc_final: 0.7790 (t0) REVERT: B 264 LYS cc_start: 0.9237 (pttm) cc_final: 0.8910 (pttm) REVERT: B 354 MET cc_start: 0.8050 (mtt) cc_final: 0.7705 (mtm) REVERT: B 431 MET cc_start: 0.9075 (mtm) cc_final: 0.8736 (mtp) REVERT: B 499 MET cc_start: 0.7115 (tmm) cc_final: 0.6781 (ppp) REVERT: B 501 MET cc_start: 0.9375 (mtm) cc_final: 0.9118 (mtm) REVERT: B 518 MET cc_start: 0.8208 (mmm) cc_final: 0.7266 (mmm) REVERT: B 541 MET cc_start: 0.8591 (mtp) cc_final: 0.7564 (tpp) REVERT: B 559 ARG cc_start: 0.8519 (ttp-170) cc_final: 0.8138 (ttt90) REVERT: B 594 GLN cc_start: 0.9016 (tp40) cc_final: 0.8408 (tp-100) REVERT: B 660 MET cc_start: 0.8603 (tpt) cc_final: 0.7985 (tpt) REVERT: B 753 TRP cc_start: 0.9285 (OUTLIER) cc_final: 0.7985 (t60) REVERT: B 794 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7707 (ttp80) REVERT: B 798 ASP cc_start: 0.8487 (t0) cc_final: 0.8266 (t0) REVERT: B 1102 MET cc_start: 0.9366 (tmm) cc_final: 0.8951 (tmm) REVERT: B 1111 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.8282 (p90) REVERT: B 1168 MET cc_start: 0.7803 (mmm) cc_final: 0.7404 (mmm) REVERT: B 1171 MET cc_start: 0.7448 (ptt) cc_final: 0.6873 (ppp) REVERT: C 1 MET cc_start: 0.7603 (tpp) cc_final: 0.7318 (tmm) REVERT: C 89 GLN cc_start: 0.8399 (pm20) cc_final: 0.8034 (pm20) REVERT: C 408 ILE cc_start: 0.9602 (mt) cc_final: 0.9294 (pt) REVERT: C 665 MET cc_start: 0.7762 (mtp) cc_final: 0.7388 (mtp) REVERT: C 667 MET cc_start: 0.6118 (ttm) cc_final: 0.5146 (ttm) REVERT: C 906 ASP cc_start: 0.8650 (m-30) cc_final: 0.8184 (t0) REVERT: D 25 LEU cc_start: 0.9394 (mt) cc_final: 0.9075 (pp) REVERT: D 100 MET cc_start: 0.9179 (mpp) cc_final: 0.8826 (mpp) REVERT: D 108 TYR cc_start: 0.6631 (OUTLIER) cc_final: 0.6200 (p90) REVERT: D 112 MET cc_start: 0.8821 (tpp) cc_final: 0.8544 (ttm) REVERT: D 278 MET cc_start: 0.8538 (mtm) cc_final: 0.8005 (ptp) REVERT: D 471 HIS cc_start: 0.8510 (m90) cc_final: 0.8020 (m-70) REVERT: D 536 MET cc_start: 0.5738 (tpt) cc_final: 0.5238 (tpp) outliers start: 77 outliers final: 45 residues processed: 234 average time/residue: 0.3108 time to fit residues: 121.4535 Evaluate side-chains 194 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 144 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 794 ARG Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 971 ASN Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 40.0000 chunk 196 optimal weight: 9.9990 chunk 135 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 262 optimal weight: 40.0000 chunk 278 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 249 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 GLN B 971 ASN B1003 ASN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 GLN C 881 ASN C 920 GLN D 50 HIS D 115 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24452 Z= 0.216 Angle : 0.572 11.144 33409 Z= 0.287 Chirality : 0.039 0.244 3673 Planarity : 0.004 0.060 4205 Dihedral : 13.792 89.166 3721 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.98 % Allowed : 12.34 % Favored : 84.68 % 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: 0.13 (0.16), residues: 2837 helix: 1.34 (0.14), residues: 1437 sheet: -0.27 (0.31), residues: 268 loop : -1.49 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 169 HIS 0.005 0.001 HIS D 289 PHE 0.013 0.001 PHE C 19 TYR 0.013 0.001 TYR B 394 ARG 0.009 0.000 ARG B 974 *********************** 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 228 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 156 time to evaluate : 2.689 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: B 123 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8745 (pm20) REVERT: B 264 LYS cc_start: 0.9260 (pttm) cc_final: 0.8966 (pttp) REVERT: B 354 MET cc_start: 0.7983 (mtt) cc_final: 0.7613 (mtm) REVERT: B 431 MET cc_start: 0.9118 (mtm) cc_final: 0.8806 (mtp) REVERT: B 501 MET cc_start: 0.9345 (mtm) cc_final: 0.9068 (mtm) REVERT: B 541 MET cc_start: 0.8514 (mtp) cc_final: 0.7458 (tpp) REVERT: B 559 ARG cc_start: 0.8621 (ttp-170) cc_final: 0.8328 (ttt90) REVERT: B 594 GLN cc_start: 0.8978 (tp40) cc_final: 0.8345 (tp-100) REVERT: B 658 MET cc_start: 0.9225 (tpp) cc_final: 0.8806 (tpp) REVERT: B 660 MET cc_start: 0.8613 (tpt) cc_final: 0.8107 (tpt) REVERT: B 753 TRP cc_start: 0.9264 (OUTLIER) cc_final: 0.7738 (t60) REVERT: B 794 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7716 (ttp80) REVERT: B 798 ASP cc_start: 0.8578 (t0) cc_final: 0.8378 (t0) REVERT: B 1111 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.8226 (p90) REVERT: B 1168 MET cc_start: 0.8046 (mmm) cc_final: 0.7629 (mmm) REVERT: B 1171 MET cc_start: 0.7806 (ptt) cc_final: 0.7270 (ppp) REVERT: C 1 MET cc_start: 0.7683 (tpp) cc_final: 0.7371 (tmm) REVERT: C 96 MET cc_start: 0.8926 (ttm) cc_final: 0.8541 (tpp) REVERT: C 408 ILE cc_start: 0.9589 (mt) cc_final: 0.9307 (pt) REVERT: C 665 MET cc_start: 0.7723 (mtp) cc_final: 0.7394 (mtm) REVERT: C 667 MET cc_start: 0.6231 (ttm) cc_final: 0.5448 (ttm) REVERT: C 906 ASP cc_start: 0.8610 (m-30) cc_final: 0.8171 (t0) REVERT: D 25 LEU cc_start: 0.9402 (mt) cc_final: 0.9100 (pp) REVERT: D 100 MET cc_start: 0.9206 (mpp) cc_final: 0.8889 (mpp) REVERT: D 112 MET cc_start: 0.8782 (tpp) cc_final: 0.8482 (ttm) REVERT: D 396 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7218 (ttm170) REVERT: D 407 MET cc_start: 0.9387 (OUTLIER) cc_final: 0.9111 (mpp) REVERT: D 471 HIS cc_start: 0.8469 (m90) cc_final: 0.7903 (m-70) REVERT: D 536 MET cc_start: 0.5853 (tpt) cc_final: 0.5272 (tpp) outliers start: 72 outliers final: 42 residues processed: 217 average time/residue: 0.3196 time to fit residues: 114.5249 Evaluate side-chains 191 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 143 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 794 ARG Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1028 SER Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 20.0000 chunk 158 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 237 optimal weight: 0.3980 chunk 192 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 249 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 881 ASN C 920 GLN D 65 HIS D 154 GLN D 471 HIS ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24452 Z= 0.262 Angle : 0.598 9.678 33409 Z= 0.303 Chirality : 0.039 0.279 3673 Planarity : 0.004 0.054 4205 Dihedral : 13.865 88.527 3720 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.06 % Allowed : 13.04 % Favored : 83.89 % 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: 0.22 (0.16), residues: 2837 helix: 1.36 (0.14), residues: 1444 sheet: -0.09 (0.31), residues: 266 loop : -1.43 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 272 HIS 0.006 0.001 HIS D 289 PHE 0.011 0.001 PHE C 193 TYR 0.014 0.001 TYR B 394 ARG 0.008 0.000 ARG B 974 *********************** 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 227 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 153 time to evaluate : 2.827 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: B 123 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8800 (pm20) REVERT: B 264 LYS cc_start: 0.9171 (pttm) cc_final: 0.8878 (pttp) REVERT: B 354 MET cc_start: 0.7999 (mtt) cc_final: 0.7653 (mtm) REVERT: B 431 MET cc_start: 0.9135 (mtm) cc_final: 0.8799 (mtp) REVERT: B 541 MET cc_start: 0.8603 (mtp) cc_final: 0.7517 (tpp) REVERT: B 559 ARG cc_start: 0.8744 (ttp-170) cc_final: 0.8449 (ttt90) REVERT: B 594 GLN cc_start: 0.8965 (tp40) cc_final: 0.8377 (tp-100) REVERT: B 658 MET cc_start: 0.9340 (tpp) cc_final: 0.8953 (tpp) REVERT: B 753 TRP cc_start: 0.9219 (OUTLIER) cc_final: 0.8062 (t60) REVERT: B 794 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7729 (ttp80) REVERT: B 798 ASP cc_start: 0.8560 (t0) cc_final: 0.8332 (t0) REVERT: B 1111 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.8409 (p90) REVERT: B 1171 MET cc_start: 0.7950 (ptt) cc_final: 0.7498 (ptt) REVERT: C 1 MET cc_start: 0.7728 (tpp) cc_final: 0.7326 (tmm) REVERT: C 42 MET cc_start: 0.7962 (tpp) cc_final: 0.7753 (tpp) REVERT: C 96 MET cc_start: 0.8973 (ttm) cc_final: 0.8580 (tpp) REVERT: C 408 ILE cc_start: 0.9602 (mt) cc_final: 0.9343 (pt) REVERT: C 610 THR cc_start: 0.9308 (p) cc_final: 0.9080 (p) REVERT: C 665 MET cc_start: 0.7735 (mtp) cc_final: 0.7421 (mtp) REVERT: C 667 MET cc_start: 0.6211 (ttm) cc_final: 0.5309 (ttm) REVERT: C 787 MET cc_start: 0.7467 (pmm) cc_final: 0.7066 (pmm) REVERT: C 906 ASP cc_start: 0.8680 (m-30) cc_final: 0.8221 (t0) REVERT: C 1048 THR cc_start: 0.9209 (OUTLIER) cc_final: 0.9000 (p) REVERT: C 1102 MET cc_start: 0.9513 (ttt) cc_final: 0.9202 (tpp) REVERT: D 25 LEU cc_start: 0.9443 (mt) cc_final: 0.9133 (pp) REVERT: D 100 MET cc_start: 0.9264 (mpp) cc_final: 0.8980 (mpp) REVERT: D 112 MET cc_start: 0.8929 (tpp) cc_final: 0.8583 (ttm) REVERT: D 396 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7291 (ttm170) REVERT: D 407 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.9092 (mpp) REVERT: D 471 HIS cc_start: 0.8617 (m170) cc_final: 0.8056 (m-70) REVERT: D 536 MET cc_start: 0.5954 (tpt) cc_final: 0.5433 (tpp) outliers start: 74 outliers final: 48 residues processed: 216 average time/residue: 0.3138 time to fit residues: 112.5264 Evaluate side-chains 198 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 143 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 794 ARG Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 6.9990 chunk 250 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 163 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 278 optimal weight: 10.0000 chunk 231 optimal weight: 20.0000 chunk 129 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 92 optimal weight: 30.0000 chunk 146 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 943 HIS B1084 ASN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 HIS D 328 GLN ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 HIS ** 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: 0.7966 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 24452 Z= 0.366 Angle : 0.712 10.854 33409 Z= 0.361 Chirality : 0.042 0.240 3673 Planarity : 0.005 0.054 4205 Dihedral : 14.215 88.277 3720 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.23 % Allowed : 13.79 % Favored : 82.98 % 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: -0.25 (0.15), residues: 2837 helix: 0.88 (0.13), residues: 1455 sheet: -0.09 (0.32), residues: 244 loop : -1.56 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 272 HIS 0.007 0.001 HIS D 289 PHE 0.017 0.002 PHE C1112 TYR 0.020 0.002 TYR C 728 ARG 0.009 0.001 ARG B 974 *********************** 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 221 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 143 time to evaluate : 2.768 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 269 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7378 (mm) REVERT: B 354 MET cc_start: 0.8046 (mtt) cc_final: 0.7726 (mtm) REVERT: B 431 MET cc_start: 0.9085 (mtm) cc_final: 0.8799 (mtp) REVERT: B 469 MET cc_start: 0.8959 (ptm) cc_final: 0.8564 (ppp) REVERT: B 541 MET cc_start: 0.8657 (mtp) cc_final: 0.7573 (tpp) REVERT: B 559 ARG cc_start: 0.8728 (ttp-170) cc_final: 0.8395 (ttt90) REVERT: B 594 GLN cc_start: 0.8954 (tp40) cc_final: 0.8345 (tp-100) REVERT: B 694 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8692 (mm) REVERT: B 753 TRP cc_start: 0.9237 (OUTLIER) cc_final: 0.8074 (t60) REVERT: B 798 ASP cc_start: 0.8570 (t0) cc_final: 0.8288 (t0) REVERT: B 1061 MET cc_start: 0.6865 (tpp) cc_final: 0.6365 (tpp) REVERT: B 1102 MET cc_start: 0.9394 (tmm) cc_final: 0.9128 (tmm) REVERT: B 1111 TYR cc_start: 0.8733 (OUTLIER) cc_final: 0.8440 (p90) REVERT: B 1168 MET cc_start: 0.8273 (mmm) cc_final: 0.7746 (mpp) REVERT: B 1171 MET cc_start: 0.8240 (ptt) cc_final: 0.7735 (ppp) REVERT: C 96 MET cc_start: 0.9041 (ttm) cc_final: 0.8646 (tpp) REVERT: C 646 ASP cc_start: 0.8803 (t0) cc_final: 0.8146 (t0) REVERT: C 665 MET cc_start: 0.7699 (mtp) cc_final: 0.7408 (mtp) REVERT: C 667 MET cc_start: 0.6466 (ttm) cc_final: 0.5589 (ttm) REVERT: C 787 MET cc_start: 0.7753 (pmm) cc_final: 0.7053 (ptp) REVERT: C 906 ASP cc_start: 0.8745 (m-30) cc_final: 0.8314 (t0) REVERT: C 1102 MET cc_start: 0.9552 (ttt) cc_final: 0.9192 (tpp) REVERT: D 100 MET cc_start: 0.9325 (mpp) cc_final: 0.9115 (mpp) REVERT: D 112 MET cc_start: 0.8950 (tpp) cc_final: 0.8614 (ttm) REVERT: D 396 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7500 (ttm170) REVERT: D 407 MET cc_start: 0.9385 (OUTLIER) cc_final: 0.9064 (mpp) REVERT: D 471 HIS cc_start: 0.9004 (m90) cc_final: 0.8612 (m90) REVERT: D 483 MET cc_start: 0.3029 (tmm) cc_final: 0.2654 (tmm) outliers start: 78 outliers final: 53 residues processed: 212 average time/residue: 0.3322 time to fit residues: 116.1990 Evaluate side-chains 191 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 132 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1028 SER Chi-restraints excluded: chain B residue 1085 TRP Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 158 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 234 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 277 optimal weight: 30.0000 chunk 173 optimal weight: 9.9990 chunk 169 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24452 Z= 0.239 Angle : 0.603 11.099 33409 Z= 0.305 Chirality : 0.040 0.179 3673 Planarity : 0.004 0.052 4205 Dihedral : 14.188 87.825 3720 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.69 % Allowed : 15.20 % Favored : 82.11 % 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: 0.10 (0.16), residues: 2837 helix: 1.26 (0.14), residues: 1451 sheet: -0.01 (0.33), residues: 231 loop : -1.50 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 841 HIS 0.004 0.001 HIS C 377 PHE 0.011 0.001 PHE D 512 TYR 0.013 0.001 TYR B 394 ARG 0.010 0.000 ARG B 794 *********************** 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 206 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 141 time to evaluate : 2.818 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 354 MET cc_start: 0.7960 (mtt) cc_final: 0.7644 (mtm) REVERT: B 431 MET cc_start: 0.9068 (mtm) cc_final: 0.8775 (mtp) REVERT: B 469 MET cc_start: 0.8944 (ptm) cc_final: 0.8545 (ppp) REVERT: B 541 MET cc_start: 0.8761 (mtp) cc_final: 0.7748 (tpp) REVERT: B 559 ARG cc_start: 0.8747 (ttp-170) cc_final: 0.8499 (ttt90) REVERT: B 594 GLN cc_start: 0.8880 (tp40) cc_final: 0.8286 (tp-100) REVERT: B 694 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8701 (mm) REVERT: B 753 TRP cc_start: 0.9212 (OUTLIER) cc_final: 0.7901 (t60) REVERT: B 1061 MET cc_start: 0.6502 (tpp) cc_final: 0.6091 (tpp) REVERT: B 1102 MET cc_start: 0.9390 (tmm) cc_final: 0.9180 (tmm) REVERT: B 1111 TYR cc_start: 0.8781 (OUTLIER) cc_final: 0.8457 (p90) REVERT: B 1168 MET cc_start: 0.8321 (mmm) cc_final: 0.7896 (mmm) REVERT: B 1171 MET cc_start: 0.8400 (ptt) cc_final: 0.8049 (ppp) REVERT: C 1 MET cc_start: 0.8086 (tpp) cc_final: 0.7780 (tmm) REVERT: C 46 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8779 (mm) REVERT: C 96 MET cc_start: 0.8972 (ttm) cc_final: 0.8626 (tpp) REVERT: C 646 ASP cc_start: 0.8873 (t0) cc_final: 0.8257 (t0) REVERT: C 665 MET cc_start: 0.7668 (mtp) cc_final: 0.7376 (mtp) REVERT: C 667 MET cc_start: 0.6310 (ttm) cc_final: 0.5550 (ttm) REVERT: C 787 MET cc_start: 0.7746 (pmm) cc_final: 0.7067 (ptp) REVERT: C 906 ASP cc_start: 0.8692 (m-30) cc_final: 0.8241 (t0) REVERT: C 1060 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8043 (p0) REVERT: D 100 MET cc_start: 0.9310 (mpp) cc_final: 0.9098 (mpp) REVERT: D 112 MET cc_start: 0.8931 (tpp) cc_final: 0.8607 (ttm) REVERT: D 149 ASP cc_start: 0.9129 (OUTLIER) cc_final: 0.8789 (p0) REVERT: D 396 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7490 (ttm170) REVERT: D 407 MET cc_start: 0.9370 (OUTLIER) cc_final: 0.9050 (mpp) REVERT: D 471 HIS cc_start: 0.9008 (m90) cc_final: 0.8495 (m-70) REVERT: D 536 MET cc_start: 0.8869 (mpp) cc_final: 0.8185 (tpt) outliers start: 65 outliers final: 50 residues processed: 199 average time/residue: 0.3242 time to fit residues: 107.8833 Evaluate side-chains 192 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 134 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1085 TRP Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1060 ASP Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 165 optimal weight: 7.9990 chunk 83 optimal weight: 30.0000 chunk 54 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 189 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 218 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 793 ASN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.6201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24452 Z= 0.242 Angle : 0.607 11.283 33409 Z= 0.305 Chirality : 0.040 0.203 3673 Planarity : 0.004 0.051 4205 Dihedral : 14.165 88.366 3720 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.06 % Allowed : 15.07 % Favored : 81.86 % 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: 0.29 (0.16), residues: 2837 helix: 1.48 (0.14), residues: 1439 sheet: -0.08 (0.32), residues: 246 loop : -1.44 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 534 HIS 0.004 0.001 HIS D 128 PHE 0.011 0.001 PHE D 512 TYR 0.013 0.001 TYR B 394 ARG 0.008 0.000 ARG B 794 *********************** 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 214 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 140 time to evaluate : 2.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7393 (mm) REVERT: B 354 MET cc_start: 0.7958 (mtt) cc_final: 0.7495 (mtm) REVERT: B 431 MET cc_start: 0.9063 (mtm) cc_final: 0.8784 (mtp) REVERT: B 469 MET cc_start: 0.8947 (ptm) cc_final: 0.8544 (ppp) REVERT: B 501 MET cc_start: 0.9349 (mtm) cc_final: 0.8560 (mpp) REVERT: B 541 MET cc_start: 0.8701 (mtp) cc_final: 0.7647 (tpp) REVERT: B 559 ARG cc_start: 0.8761 (ttp-170) cc_final: 0.8419 (ttt90) REVERT: B 594 GLN cc_start: 0.8797 (tp40) cc_final: 0.8254 (tp-100) REVERT: B 660 MET cc_start: 0.8337 (tpt) cc_final: 0.7589 (tpt) REVERT: B 694 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8693 (mm) REVERT: B 753 TRP cc_start: 0.9224 (OUTLIER) cc_final: 0.7864 (t60) REVERT: B 798 ASP cc_start: 0.8290 (t0) cc_final: 0.8071 (t0) REVERT: B 1111 TYR cc_start: 0.8781 (OUTLIER) cc_final: 0.8458 (p90) REVERT: B 1171 MET cc_start: 0.8542 (ptt) cc_final: 0.8136 (ptt) REVERT: C 96 MET cc_start: 0.8944 (ttm) cc_final: 0.8596 (tpp) REVERT: C 387 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8660 (mm-30) REVERT: C 646 ASP cc_start: 0.8888 (t0) cc_final: 0.8283 (t0) REVERT: C 665 MET cc_start: 0.7712 (mtp) cc_final: 0.7364 (mtp) REVERT: C 667 MET cc_start: 0.6319 (ttm) cc_final: 0.5554 (ttm) REVERT: C 787 MET cc_start: 0.7724 (pmm) cc_final: 0.7073 (ptp) REVERT: C 906 ASP cc_start: 0.8663 (m-30) cc_final: 0.8217 (t0) REVERT: C 1060 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8043 (p0) REVERT: C 1102 MET cc_start: 0.9423 (ttt) cc_final: 0.9047 (tpp) REVERT: D 100 MET cc_start: 0.9350 (mpp) cc_final: 0.9130 (mpp) REVERT: D 112 MET cc_start: 0.8931 (tpp) cc_final: 0.8609 (ttm) REVERT: D 149 ASP cc_start: 0.9099 (OUTLIER) cc_final: 0.8804 (p0) REVERT: D 396 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7494 (ttm170) REVERT: D 407 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.9023 (mpp) REVERT: D 439 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8412 (pm20) REVERT: D 471 HIS cc_start: 0.9120 (m90) cc_final: 0.8748 (m90) REVERT: D 536 MET cc_start: 0.9031 (mpp) cc_final: 0.8143 (tpt) outliers start: 74 outliers final: 49 residues processed: 206 average time/residue: 0.3334 time to fit residues: 114.6061 Evaluate side-chains 194 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 136 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 1085 TRP Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1060 ASP Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 439 GLN Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 20.0000 chunk 265 optimal weight: 7.9990 chunk 242 optimal weight: 30.0000 chunk 258 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 203 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 233 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 257 optimal weight: 8.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.6472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 24452 Z= 0.296 Angle : 0.656 11.803 33409 Z= 0.328 Chirality : 0.040 0.195 3673 Planarity : 0.004 0.051 4205 Dihedral : 14.196 89.223 3716 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.86 % Allowed : 15.69 % Favored : 81.45 % 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: 0.18 (0.16), residues: 2837 helix: 1.33 (0.14), residues: 1446 sheet: -0.16 (0.32), residues: 247 loop : -1.42 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B1085 HIS 0.007 0.001 HIS B 689 PHE 0.013 0.002 PHE C 193 TYR 0.015 0.002 TYR C 728 ARG 0.007 0.001 ARG B 794 *********************** 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 203 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 134 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7501 (mm) REVERT: B 354 MET cc_start: 0.7982 (mtt) cc_final: 0.7503 (mtm) REVERT: B 431 MET cc_start: 0.9053 (mtm) cc_final: 0.8786 (mtp) REVERT: B 469 MET cc_start: 0.8950 (ptm) cc_final: 0.8567 (ppp) REVERT: B 501 MET cc_start: 0.9372 (mtm) cc_final: 0.8510 (mpp) REVERT: B 518 MET cc_start: 0.8633 (mmm) cc_final: 0.8359 (mmm) REVERT: B 541 MET cc_start: 0.8699 (mtp) cc_final: 0.7630 (tpp) REVERT: B 559 ARG cc_start: 0.8787 (ttp-170) cc_final: 0.8430 (ttt90) REVERT: B 620 MET cc_start: 0.8563 (pmm) cc_final: 0.8294 (pmm) REVERT: B 694 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8719 (mm) REVERT: B 753 TRP cc_start: 0.9231 (OUTLIER) cc_final: 0.7847 (t60) REVERT: B 1111 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.8450 (p90) REVERT: B 1171 MET cc_start: 0.8633 (ptt) cc_final: 0.8350 (ppp) REVERT: C 96 MET cc_start: 0.8974 (ttm) cc_final: 0.8656 (tpp) REVERT: C 387 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8534 (mm-30) REVERT: C 646 ASP cc_start: 0.8918 (t0) cc_final: 0.8322 (t0) REVERT: C 665 MET cc_start: 0.7794 (mtp) cc_final: 0.7485 (mtp) REVERT: C 667 MET cc_start: 0.6356 (ttm) cc_final: 0.5518 (ttm) REVERT: C 787 MET cc_start: 0.7631 (pmm) cc_final: 0.7067 (ptp) REVERT: C 906 ASP cc_start: 0.8693 (m-30) cc_final: 0.8243 (t0) REVERT: C 1060 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8061 (p0) REVERT: C 1102 MET cc_start: 0.9430 (ttt) cc_final: 0.9005 (tpp) REVERT: D 100 MET cc_start: 0.9382 (mpp) cc_final: 0.9066 (mmm) REVERT: D 112 MET cc_start: 0.8933 (tpp) cc_final: 0.8610 (ttm) REVERT: D 149 ASP cc_start: 0.9065 (OUTLIER) cc_final: 0.8750 (p0) REVERT: D 278 MET cc_start: 0.8314 (mtm) cc_final: 0.7853 (mtm) REVERT: D 279 MET cc_start: 0.8918 (ptp) cc_final: 0.8655 (ptp) REVERT: D 396 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7520 (ttm170) REVERT: D 407 MET cc_start: 0.9392 (OUTLIER) cc_final: 0.9054 (mpp) REVERT: D 439 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8410 (pm20) REVERT: D 471 HIS cc_start: 0.9167 (m90) cc_final: 0.8864 (m-70) outliers start: 69 outliers final: 50 residues processed: 197 average time/residue: 0.3166 time to fit residues: 103.8681 Evaluate side-chains 189 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 130 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 1085 TRP Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1060 ASP Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain D residue 439 GLN Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 10.0000 chunk 273 optimal weight: 9.9990 chunk 166 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 190 optimal weight: 8.9990 chunk 286 optimal weight: 20.0000 chunk 264 optimal weight: 9.9990 chunk 228 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 176 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 overall best weight: 6.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 GLN ** C 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.6889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 24452 Z= 0.327 Angle : 0.686 12.931 33409 Z= 0.345 Chirality : 0.042 0.232 3673 Planarity : 0.004 0.049 4205 Dihedral : 14.365 88.189 3716 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.61 % Allowed : 15.78 % Favored : 81.61 % 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: -0.02 (0.16), residues: 2837 helix: 1.12 (0.14), residues: 1441 sheet: -0.15 (0.33), residues: 234 loop : -1.45 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 534 HIS 0.005 0.001 HIS C 377 PHE 0.014 0.002 PHE C 193 TYR 0.017 0.002 TYR C 138 ARG 0.006 0.001 ARG B 794 ********************** 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 198 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 135 time to evaluate : 2.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.8127 (ppp) cc_final: 0.7722 (ppp) REVERT: B 269 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7643 (mm) REVERT: B 354 MET cc_start: 0.7979 (mtt) cc_final: 0.7495 (mtm) REVERT: B 431 MET cc_start: 0.9029 (mtm) cc_final: 0.8798 (mtp) REVERT: B 501 MET cc_start: 0.9372 (mtm) cc_final: 0.8496 (mpp) REVERT: B 541 MET cc_start: 0.8668 (mtp) cc_final: 0.7604 (tpp) REVERT: B 559 ARG cc_start: 0.8815 (ttp-170) cc_final: 0.8487 (ttt90) REVERT: B 694 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8699 (mm) REVERT: B 753 TRP cc_start: 0.9189 (OUTLIER) cc_final: 0.7910 (t60) REVERT: B 1021 MET cc_start: 0.9110 (tpp) cc_final: 0.8752 (tpp) REVERT: B 1111 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.8439 (p90) REVERT: B 1171 MET cc_start: 0.8736 (ptt) cc_final: 0.8474 (ppp) REVERT: C 96 MET cc_start: 0.8961 (ttm) cc_final: 0.8639 (tpp) REVERT: C 602 ASP cc_start: 0.8731 (t0) cc_final: 0.8466 (t70) REVERT: C 646 ASP cc_start: 0.8935 (t0) cc_final: 0.8330 (t0) REVERT: C 665 MET cc_start: 0.7682 (mtp) cc_final: 0.7418 (mtp) REVERT: C 667 MET cc_start: 0.6228 (ttm) cc_final: 0.5422 (ttm) REVERT: C 787 MET cc_start: 0.7693 (pmm) cc_final: 0.7158 (ptp) REVERT: C 906 ASP cc_start: 0.8739 (m-30) cc_final: 0.8224 (t0) REVERT: C 1060 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8089 (p0) REVERT: C 1102 MET cc_start: 0.9449 (ttt) cc_final: 0.9012 (tpp) REVERT: D 100 MET cc_start: 0.9396 (mpp) cc_final: 0.9045 (mmm) REVERT: D 112 MET cc_start: 0.8949 (tpp) cc_final: 0.8616 (ttm) REVERT: D 149 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8713 (p0) REVERT: D 396 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7686 (ttt-90) REVERT: D 407 MET cc_start: 0.9408 (OUTLIER) cc_final: 0.9200 (mpp) REVERT: D 439 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8350 (pm20) REVERT: D 471 HIS cc_start: 0.9257 (m90) cc_final: 0.8957 (m-70) REVERT: D 536 MET cc_start: 0.8203 (mmm) cc_final: 0.7432 (tpt) outliers start: 63 outliers final: 52 residues processed: 192 average time/residue: 0.3107 time to fit residues: 100.1513 Evaluate side-chains 194 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 133 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 610 ASN Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 1085 TRP Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1060 ASP Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain D residue 439 GLN Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 4.9990 chunk 243 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 210 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 ASN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.063229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.046062 restraints weight = 158466.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.047498 restraints weight = 93028.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.048406 restraints weight = 66393.881| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.6890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24452 Z= 0.225 Angle : 0.619 14.969 33409 Z= 0.308 Chirality : 0.040 0.188 3673 Planarity : 0.004 0.051 4205 Dihedral : 14.317 87.526 3716 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.40 % Allowed : 16.02 % Favored : 81.57 % 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: 0.25 (0.16), residues: 2837 helix: 1.42 (0.14), residues: 1433 sheet: -0.04 (0.33), residues: 239 loop : -1.40 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 534 HIS 0.005 0.001 HIS C 377 PHE 0.011 0.001 PHE C 193 TYR 0.013 0.001 TYR C 256 ARG 0.007 0.000 ARG B 794 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4122.34 seconds wall clock time: 75 minutes 39.14 seconds (4539.14 seconds total)