Starting phenix.real_space_refine on Mon Feb 19 05:42:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjf_10216/02_2024/6sjf_10216.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjf_10216/02_2024/6sjf_10216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjf_10216/02_2024/6sjf_10216.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjf_10216/02_2024/6sjf_10216.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjf_10216/02_2024/6sjf_10216.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjf_10216/02_2024/6sjf_10216.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 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 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 396": "NH1" <-> "NH2" Residue "D ARG 417": "NH1" <-> "NH2" Residue "D ARG 470": "NH1" <-> "NH2" Residue "D ARG 475": "NH1" <-> "NH2" Residue "D PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 509": "NH1" <-> "NH2" Residue "D PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 526": "NH1" <-> "NH2" Residue "D ARG 557": "NH1" <-> "NH2" Residue "D ARG 574": "NH1" <-> "NH2" Residue "D ARG 576": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 14.55, per 1000 atoms: 0.61 Number of scatterers: 23826 At special positions: 0 Unit cell: (151.815, 151.815, 123.546, 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: 9.06 Conformation dependent library (CDL) restraints added in 4.1 seconds 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5372 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 16 sheets defined 53.4% alpha, 9.1% beta 17 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 8.65 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: 3.553A pdb=" N GLU B 58 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 3.624A 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: 3.720A 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: 3.607A pdb=" N SER B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 173 removed outlier: 3.794A pdb=" N TYR B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.278A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 3.667A pdb=" N LEU B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 239 removed outlier: 3.565A 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: 3.632A pdb=" N ASN B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.854A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 317 removed outlier: 4.333A pdb=" N GLU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 4.518A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.538A pdb=" N MET B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 4.130A 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: 3.755A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.811A 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 removed outlier: 3.515A pdb=" N LEU B 573 " --> pdb=" O ASP B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 590 through 605 removed outlier: 3.905A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.867A 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: 3.581A pdb=" N TRP B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 668 removed outlier: 3.903A pdb=" N MET B 660 " --> pdb=" O GLY B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 677 removed outlier: 3.541A pdb=" N ASN B 673 " --> pdb=" O ASN B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 699 removed outlier: 3.539A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 717 removed outlier: 3.833A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 807 removed outlier: 3.543A pdb=" N GLU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 836 removed outlier: 4.539A pdb=" N HIS B 834 " --> pdb=" O THR B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 843 removed outlier: 3.787A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 860 removed outlier: 3.928A 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: 3.705A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1012 removed outlier: 3.703A pdb=" N GLN B1011 " --> pdb=" O SER B1008 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B1012 " --> pdb=" O LEU B1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1008 through 1012' Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 3.650A pdb=" N THR B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1048 removed outlier: 3.789A 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 Processing helix chain 'C' and resid 9 through 24 removed outlier: 4.153A 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: 3.716A 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: 3.850A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.841A 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 removed outlier: 3.551A pdb=" N LEU C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 232 removed outlier: 3.627A pdb=" N ALA C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.673A pdb=" N LYS C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 333 through 344 Processing helix chain 'C' and resid 354 through 360 removed outlier: 3.509A pdb=" N ARG C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 400 removed outlier: 3.665A pdb=" N VAL C 386 " --> pdb=" O PRO C 382 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP C 391 " --> pdb=" O GLU C 387 " (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: 3.723A 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: 3.926A pdb=" N ALA C 453 " --> pdb=" O PRO C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 476 through 483 removed outlier: 3.639A pdb=" N PHE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 501 removed outlier: 3.763A pdb=" N GLN C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY C 501 " --> pdb=" O VAL C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 Processing helix chain 'C' and resid 523 through 537 Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.683A pdb=" N MET C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 599 removed outlier: 4.493A pdb=" N CYS C 591 " --> pdb=" O TRP C 587 " (cutoff:3.500A) removed outlier: 4.504A 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: 3.773A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 3.796A 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 803 through 805 No H-bonds generated for 'chain 'C' and resid 803 through 805' Processing helix chain 'C' and resid 806 through 812 Processing helix chain 'C' and resid 833 through 843 removed outlier: 3.515A pdb=" N LEU C 837 " --> pdb=" O PRO C 833 " (cutoff:3.500A) removed outlier: 3.760A 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: 3.629A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 932 removed outlier: 3.748A pdb=" N GLU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 3.822A 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: 3.562A pdb=" N GLY C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1033 removed outlier: 3.940A 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: 3.532A pdb=" N ARG C1068 " --> pdb=" O LEU C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1089 through 1094 removed outlier: 4.288A 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: 3.873A pdb=" N PHE C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.688A 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: 3.972A pdb=" N SER D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 125 Processing helix chain 'D' and resid 133 through 145 Processing helix chain 'D' and resid 152 through 164 removed outlier: 3.605A 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: 3.603A 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: 3.594A pdb=" N MET D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 285 removed outlier: 3.579A pdb=" N ALA D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 315 removed outlier: 3.829A pdb=" N ASP D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 319 removed outlier: 3.536A pdb=" N ALA D 319 " --> pdb=" O TYR D 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 316 through 319' Processing helix chain 'D' and resid 322 through 334 removed outlier: 3.557A 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: 3.905A pdb=" N GLN D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.586A pdb=" N ALA D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 391 removed outlier: 3.889A pdb=" N THR D 391 " --> pdb=" O GLN D 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 388 through 391' Processing helix chain 'D' and resid 400 through 415 Processing helix chain 'D' and resid 415 through 424 Processing helix chain 'D' and resid 427 through 436 removed outlier: 3.528A pdb=" N ILE D 431 " --> pdb=" O GLU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 465 Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.503A 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: 3.678A pdb=" N ILE D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 3.776A 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: 6.380A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA B 439 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 20 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 6.078A 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: 6.788A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL B 62 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 5.808A 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: 6.366A 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: 6.433A pdb=" N VAL B 207 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA5, first strand: chain 'B' and resid 487 through 490 Processing sheet with id=AA6, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.603A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE B 554 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N VAL B 739 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1017 through 1027 removed outlier: 6.656A pdb=" N ASP B1067 " --> pdb=" O GLU B1020 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLU B1022 " --> pdb=" O PHE B1065 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N PHE B1065 " --> pdb=" O GLU B1022 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR B1024 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LYS B1063 " --> pdb=" O TYR B1024 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N MET B1061 " --> pdb=" O PRO B1026 " (cutoff:3.500A) removed outlier: 10.028A pdb=" N ILE B1066 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N TYR B1081 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N TYR B1076 " --> pdb=" O GLY B1137 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N ILE B1139 " --> pdb=" O TYR B1076 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU B1078 " --> pdb=" O ILE B1139 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU B1141 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA B1080 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.007A pdb=" N ARG C 266 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.000A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 437 through 439 removed outlier: 3.591A pdb=" N ASN C 660 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LYS C 673 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N TYR C 728 " --> pdb=" O LYS C 673 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 9.095A pdb=" N CYS C 782 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N PHE C 376 " --> pdb=" O CYS C 782 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 939 through 947 removed outlier: 5.633A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 15.501A pdb=" N LEU C 956 " --> pdb=" O TRP C 967 " (cutoff:3.500A) removed outlier: 13.137A pdb=" N TRP C 967 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLN C 958 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LEU C 965 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.335A 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: 3.531A 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: 6.042A 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: 3.579A pdb=" N GLY D 296 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU D 266 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU D 295 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL D 268 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG D 200 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N SER D 238 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.527A 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: 7.251A pdb=" N ASP D 547 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.391A 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: 4.447A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) 1062 hydrogen bonds defined for protein. 3126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 10.07 Time building geometry restraints manager: 9.87 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: 6864 1.34 - 1.45: 4231 1.45 - 1.57: 13082 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 1.481 -0.024 1.29e-02 6.01e+03 3.45e+00 bond pdb=" CA PRO B1051 " pdb=" C PRO B1051 " ideal model delta sigma weight residual 1.514 1.505 0.010 5.50e-03 3.31e+04 3.17e+00 bond pdb=" C LEU C 460 " pdb=" N PRO C 461 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.23e-02 6.61e+03 2.89e+00 bond pdb=" C HIS C 448 " pdb=" N PRO C 449 " ideal model delta sigma weight residual 1.337 1.353 -0.016 9.80e-03 1.04e+04 2.73e+00 bond pdb=" C LEU D 276 " pdb=" N PRO D 277 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.20e-02 6.94e+03 2.70e+00 ... (remaining 24447 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.26: 995 106.26 - 113.20: 12933 113.20 - 120.14: 8943 120.14 - 127.08: 10125 127.08 - 134.02: 413 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 121.54 129.95 -8.41 1.91e+00 2.74e-01 1.94e+01 angle pdb=" C ASN B1084 " pdb=" N TRP B1085 " pdb=" CA TRP B1085 " ideal model delta sigma weight residual 122.82 127.50 -4.68 1.42e+00 4.96e-01 1.09e+01 angle pdb=" N ILE B 266 " pdb=" CA ILE B 266 " pdb=" C ILE B 266 " ideal model delta sigma weight residual 106.21 109.57 -3.36 1.07e+00 8.73e-01 9.85e+00 angle pdb=" C VAL B 657 " pdb=" N MET B 658 " pdb=" CA MET B 658 " ideal model delta sigma weight residual 120.09 123.98 -3.89 1.25e+00 6.40e-01 9.69e+00 angle pdb=" C GLN D 387 " pdb=" N GLN D 388 " pdb=" CA GLN D 388 " ideal model delta sigma weight residual 121.54 127.45 -5.91 1.91e+00 2.74e-01 9.57e+00 ... (remaining 33404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.85: 13327 15.85 - 31.70: 824 31.70 - 47.54: 330 47.54 - 63.39: 123 63.39 - 79.24: 11 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 -160.49 -19.51 0 5.00e+00 4.00e-02 1.52e+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 180.00 162.72 17.28 0 5.00e+00 4.00e-02 1.19e+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 180.00 163.78 16.22 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 14612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2596 0.034 - 0.069: 764 0.069 - 0.103: 217 0.103 - 0.138: 85 0.138 - 0.172: 11 Chirality restraints: 3673 Sorted by residual: chirality pdb=" CA LEU C 588 " pdb=" N LEU C 588 " pdb=" C LEU C 588 " pdb=" CB LEU C 588 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" CA MET B 469 " pdb=" N MET B 469 " pdb=" C MET B 469 " pdb=" CB MET B 469 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CA TYR B 173 " pdb=" N TYR B 173 " pdb=" C TYR B 173 " pdb=" CB TYR B 173 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 3670 not shown) Planarity restraints: 4205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " -0.052 5.00e-02 4.00e+02 7.88e-02 9.93e+00 pdb=" N PRO C 658 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 419 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO C 420 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 420 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 420 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 304 " 0.036 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO B 305 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 305 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 305 " 0.030 5.00e-02 4.00e+02 ... (remaining 4202 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 7111 2.83 - 3.34: 19854 3.34 - 3.86: 39686 3.86 - 4.38: 44623 4.38 - 4.90: 76485 Nonbonded interactions: 187759 Sorted by model distance: nonbonded pdb=" O THR D 533 " pdb=" OG1 THR D 533 " model vdw 2.307 2.440 nonbonded pdb=" O2 DC X 27 " pdb=" N2 DG X 59 " model vdw 2.308 2.496 nonbonded pdb=" O LEU C 115 " pdb=" OG SER C 119 " model vdw 2.324 2.440 nonbonded pdb=" O LEU D 67 " pdb=" OG1 THR D 70 " model vdw 2.336 2.440 nonbonded pdb=" OH TYR C 794 " pdb=" O ALA C 803 " model vdw 2.338 2.440 ... (remaining 187754 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.210 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 71.070 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24452 Z= 0.166 Angle : 0.574 8.406 33409 Z= 0.344 Chirality : 0.039 0.172 3673 Planarity : 0.005 0.079 4205 Dihedral : 13.121 79.239 9243 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.98 % Allowed : 4.89 % Favored : 92.13 % 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: -3.64 (0.11), residues: 2837 helix: -2.57 (0.09), residues: 1397 sheet: -0.77 (0.29), residues: 276 loop : -2.47 (0.14), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 164 HIS 0.004 0.000 HIS D 256 PHE 0.015 0.001 PHE B1023 TYR 0.014 0.001 TYR B1093 ARG 0.003 0.000 ARG B 761 *********************** 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 711 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 639 time to evaluate : 2.893 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: B 137 LEU cc_start: 0.8882 (mt) cc_final: 0.8599 (mp) REVERT: B 138 ASN cc_start: 0.8379 (m-40) cc_final: 0.7947 (m110) REVERT: B 351 PHE cc_start: 0.7831 (m-80) cc_final: 0.6838 (m-10) REVERT: B 354 MET cc_start: 0.7846 (mtt) cc_final: 0.7618 (mtm) REVERT: B 491 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7600 (t80) REVERT: B 501 MET cc_start: 0.8652 (mtm) cc_final: 0.8255 (mtt) REVERT: B 582 SER cc_start: 0.8875 (m) cc_final: 0.8538 (t) REVERT: B 595 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7449 (mt-10) REVERT: B 753 TRP cc_start: 0.9163 (OUTLIER) cc_final: 0.7804 (t60) REVERT: B 758 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.8985 (p) REVERT: B 1111 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.8063 (p90) REVERT: C 2 LEU cc_start: 0.7036 (tp) cc_final: 0.6791 (tp) REVERT: C 103 LEU cc_start: 0.8679 (mt) cc_final: 0.8278 (mt) REVERT: C 133 ASP cc_start: 0.7700 (t0) cc_final: 0.7319 (t0) REVERT: C 906 ASP cc_start: 0.8047 (m-30) cc_final: 0.7803 (m-30) REVERT: C 916 PHE cc_start: 0.8137 (m-80) cc_final: 0.7632 (m-80) REVERT: C 965 LEU cc_start: 0.8815 (tp) cc_final: 0.8345 (tp) REVERT: D 236 ASP cc_start: 0.6962 (OUTLIER) cc_final: 0.6139 (t0) REVERT: D 405 ILE cc_start: 0.8762 (mt) cc_final: 0.8446 (mm) REVERT: D 407 MET cc_start: 0.8947 (ttp) cc_final: 0.8718 (ppp) REVERT: D 436 ASN cc_start: 0.8254 (m-40) cc_final: 0.7247 (t0) outliers start: 72 outliers final: 12 residues processed: 690 average time/residue: 0.4056 time to fit residues: 415.4733 Evaluate side-chains 307 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 290 time to evaluate : 2.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 538 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 10.0000 chunk 218 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 147 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 225 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 261 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN B 181 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 ASN B 458 ASN B 463 GLN B 566 GLN B 594 GLN B 601 GLN B 650 GLN B 765 GLN B 843 GLN B 848 GLN B 943 HIS B 944 GLN B1003 ASN B1072 HIS B1084 ASN B1134 HIS B1161 ASN C 113 HIS C 126 GLN C 162 GLN C 185 HIS C 570 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 GLN C 660 ASN C 725 GLN C 759 HIS C 792 GLN ** C 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 GLN C 843 HIS C 856 ASN C 883 GLN C 925 GLN C 979 GLN C 993 ASN C1110 GLN D 89 GLN D 115 ASN D 222 GLN D 251 GLN D 469 HIS ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 24452 Z= 0.262 Angle : 0.634 10.974 33409 Z= 0.316 Chirality : 0.041 0.253 3673 Planarity : 0.004 0.059 4205 Dihedral : 13.503 83.708 3732 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.69 % Allowed : 12.13 % Favored : 84.18 % 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: -1.11 (0.14), residues: 2837 helix: 0.07 (0.13), residues: 1422 sheet: -0.32 (0.30), residues: 279 loop : -1.84 (0.16), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 574 HIS 0.007 0.001 HIS C 113 PHE 0.026 0.002 PHE B 397 TYR 0.014 0.001 TYR C 628 ARG 0.008 0.001 ARG D 504 *********************** 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 373 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 284 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 ILE cc_start: 0.9436 (pt) cc_final: 0.9210 (mt) REVERT: B 137 LEU cc_start: 0.8956 (mt) cc_final: 0.8325 (tp) REVERT: B 146 MET cc_start: 0.7283 (ttp) cc_final: 0.6576 (ttp) REVERT: B 351 PHE cc_start: 0.7910 (m-80) cc_final: 0.7579 (m-10) REVERT: B 354 MET cc_start: 0.7949 (mtt) cc_final: 0.7626 (mtm) REVERT: B 393 GLN cc_start: 0.8708 (mt0) cc_final: 0.8375 (mt0) REVERT: B 491 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7586 (t80) REVERT: B 738 ILE cc_start: 0.8520 (mt) cc_final: 0.8217 (pt) REVERT: B 753 TRP cc_start: 0.9194 (OUTLIER) cc_final: 0.7756 (t60) REVERT: B 758 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.8948 (t) REVERT: B 1111 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.8012 (p90) REVERT: C 2 LEU cc_start: 0.7733 (tp) cc_final: 0.7408 (tp) REVERT: C 133 ASP cc_start: 0.7728 (t0) cc_final: 0.7520 (t0) REVERT: C 499 GLU cc_start: 0.7621 (mp0) cc_final: 0.7411 (mp0) REVERT: C 965 LEU cc_start: 0.8881 (tp) cc_final: 0.8639 (tp) REVERT: C 971 LEU cc_start: 0.8624 (mt) cc_final: 0.8241 (mp) REVERT: D 143 LYS cc_start: 0.9173 (mmmt) cc_final: 0.8747 (mmtm) REVERT: D 407 MET cc_start: 0.9043 (ttp) cc_final: 0.8695 (tmm) REVERT: D 420 ASP cc_start: 0.8268 (t0) cc_final: 0.7875 (t0) REVERT: D 514 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.7247 (mpp) outliers start: 89 outliers final: 51 residues processed: 356 average time/residue: 0.3365 time to fit residues: 192.2875 Evaluate side-chains 285 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 229 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 843 GLN Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 905 SER Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1063 LYS Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 793 ASN Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 514 MET Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 562 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 217 optimal weight: 9.9990 chunk 178 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 262 optimal weight: 30.0000 chunk 283 optimal weight: 10.0000 chunk 233 optimal weight: 4.9990 chunk 259 optimal weight: 9.9990 chunk 89 optimal weight: 0.0040 chunk 210 optimal weight: 9.9990 overall best weight: 5.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS B 496 GLN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 GLN ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN C 237 HIS C 510 ASN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 749 GLN ** C 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 891 GLN C 984 HIS C1108 GLN D 22 GLN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 24452 Z= 0.390 Angle : 0.707 10.765 33409 Z= 0.354 Chirality : 0.042 0.171 3673 Planarity : 0.005 0.072 4205 Dihedral : 13.566 89.191 3715 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.47 % Allowed : 12.51 % Favored : 83.02 % 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: -0.19 (0.15), residues: 2837 helix: 0.95 (0.14), residues: 1419 sheet: -0.27 (0.30), residues: 290 loop : -1.49 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 574 HIS 0.005 0.001 HIS C 233 PHE 0.024 0.002 PHE C 672 TYR 0.020 0.002 TYR C 878 ARG 0.005 0.001 ARG C 786 *********************** 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 334 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 226 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.9030 (pttm) cc_final: 0.8812 (pttm) REVERT: B 354 MET cc_start: 0.7947 (mtt) cc_final: 0.7596 (mtm) REVERT: B 365 GLU cc_start: 0.8032 (pm20) cc_final: 0.7822 (pm20) REVERT: B 491 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.8088 (t80) REVERT: B 596 MET cc_start: 0.8405 (mtt) cc_final: 0.8152 (mtt) REVERT: B 709 ARG cc_start: 0.8287 (tpt90) cc_final: 0.8020 (tpm170) REVERT: B 753 TRP cc_start: 0.9272 (OUTLIER) cc_final: 0.7791 (t60) REVERT: B 1061 MET cc_start: 0.8107 (mmt) cc_final: 0.7774 (mmp) REVERT: B 1098 MET cc_start: 0.7128 (mpp) cc_final: 0.6634 (mpp) REVERT: B 1111 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.8086 (p90) REVERT: C 133 ASP cc_start: 0.7750 (t0) cc_final: 0.7518 (t0) REVERT: C 499 GLU cc_start: 0.7744 (mp0) cc_final: 0.7504 (mp0) REVERT: C 696 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9095 (mm) REVERT: C 790 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8462 (t0) REVERT: C 1075 TYR cc_start: 0.8497 (t80) cc_final: 0.8171 (t80) REVERT: D 112 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8202 (ttm) REVERT: D 314 CYS cc_start: 0.9140 (m) cc_final: 0.8879 (m) REVERT: D 407 MET cc_start: 0.9071 (ttp) cc_final: 0.8818 (tmm) REVERT: D 420 ASP cc_start: 0.8469 (t0) cc_final: 0.8013 (t0) REVERT: D 514 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.6757 (mpp) REVERT: D 567 TYR cc_start: 0.8468 (t80) cc_final: 0.8065 (t80) outliers start: 108 outliers final: 69 residues processed: 313 average time/residue: 0.3453 time to fit residues: 173.6303 Evaluate side-chains 272 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 196 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 721 ASN Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 843 GLN Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 905 SER Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1063 LYS Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 770 ASP Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 793 ASN Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 514 MET Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 562 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: 9.9990 chunk 196 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 262 optimal weight: 3.9990 chunk 278 optimal weight: 20.0000 chunk 137 optimal weight: 9.9990 chunk 249 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 594 GLN B 610 ASN B 843 GLN ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24452 Z= 0.197 Angle : 0.579 11.628 33409 Z= 0.285 Chirality : 0.039 0.225 3673 Planarity : 0.004 0.051 4205 Dihedral : 13.560 86.903 3714 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.64 % Allowed : 13.75 % Favored : 82.61 % 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: 0.27 (0.16), residues: 2837 helix: 1.44 (0.14), residues: 1413 sheet: -0.14 (0.30), residues: 295 loop : -1.39 (0.17), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 574 HIS 0.004 0.001 HIS B1134 PHE 0.014 0.001 PHE B 428 TYR 0.016 0.001 TYR B1093 ARG 0.004 0.000 ARG C 210 *********************** 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 321 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 233 time to evaluate : 2.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.7844 (mtt) cc_final: 0.7486 (mtm) REVERT: B 491 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7968 (t80) REVERT: B 499 MET cc_start: 0.7995 (tpt) cc_final: 0.7651 (tpt) REVERT: B 575 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7975 (pm20) REVERT: B 753 TRP cc_start: 0.9266 (OUTLIER) cc_final: 0.7863 (t60) REVERT: B 1061 MET cc_start: 0.8165 (mmt) cc_final: 0.7801 (mmp) REVERT: B 1111 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.8051 (p90) REVERT: C 1 MET cc_start: 0.6272 (tpp) cc_final: 0.6002 (tpt) REVERT: C 133 ASP cc_start: 0.7705 (t0) cc_final: 0.7498 (t0) REVERT: C 499 GLU cc_start: 0.7778 (mp0) cc_final: 0.7510 (mp0) REVERT: C 696 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9103 (mm) REVERT: C 790 ASP cc_start: 0.8843 (OUTLIER) cc_final: 0.8460 (t0) REVERT: C 916 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7651 (t80) REVERT: C 971 LEU cc_start: 0.8617 (mt) cc_final: 0.8237 (mp) REVERT: C 1075 TYR cc_start: 0.8304 (t80) cc_final: 0.8057 (t80) REVERT: C 1110 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7922 (mm110) REVERT: D 143 LYS cc_start: 0.9199 (mmmt) cc_final: 0.8764 (mmtm) REVERT: D 314 CYS cc_start: 0.9151 (m) cc_final: 0.8883 (m) REVERT: D 407 MET cc_start: 0.9054 (ttp) cc_final: 0.8736 (tmm) REVERT: D 420 ASP cc_start: 0.8577 (t0) cc_final: 0.8094 (t0) REVERT: D 514 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.6987 (mpp) REVERT: D 567 TYR cc_start: 0.8236 (t80) cc_final: 0.7724 (t80) outliers start: 88 outliers final: 60 residues processed: 303 average time/residue: 0.3403 time to fit residues: 166.2021 Evaluate side-chains 266 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 197 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 843 GLN Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 905 SER Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1063 LYS Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 770 ASP Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 793 ASN Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 916 PHE Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1088 ILE Chi-restraints excluded: chain C residue 1102 MET Chi-restraints excluded: chain C residue 1110 GLN Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 387 GLN Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 514 MET Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 561 VAL 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: 10.0000 chunk 158 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 237 optimal weight: 20.0000 chunk 192 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 249 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 ASN B 455 ASN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 HIS B 843 GLN ** B 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 951 GLN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.154 24452 Z= 0.580 Angle : 0.849 11.435 33409 Z= 0.424 Chirality : 0.046 0.176 3673 Planarity : 0.006 0.049 4205 Dihedral : 13.891 88.133 3714 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 5.05 % Allowed : 14.41 % Favored : 80.54 % 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: -0.34 (0.15), residues: 2837 helix: 0.81 (0.14), residues: 1436 sheet: -0.46 (0.29), residues: 297 loop : -1.52 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 272 HIS 0.009 0.002 HIS C 984 PHE 0.026 0.003 PHE B 475 TYR 0.025 0.003 TYR D 359 ARG 0.005 0.001 ARG B 808 *********************** 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 318 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 196 time to evaluate : 2.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.7994 (mtt) cc_final: 0.7687 (mtm) REVERT: B 518 MET cc_start: 0.9078 (mmm) cc_final: 0.8829 (mmm) REVERT: B 753 TRP cc_start: 0.9337 (OUTLIER) cc_final: 0.7916 (t60) REVERT: B 841 LEU cc_start: 0.9229 (mt) cc_final: 0.9017 (mt) REVERT: B 843 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8223 (pm20) REVERT: B 1098 MET cc_start: 0.7033 (mpp) cc_final: 0.6637 (mpp) REVERT: B 1111 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.8123 (p90) REVERT: C 2 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7440 (tp) REVERT: C 133 ASP cc_start: 0.7911 (t0) cc_final: 0.7618 (t0) REVERT: C 499 GLU cc_start: 0.7865 (mp0) cc_final: 0.7589 (mp0) REVERT: C 696 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9230 (mm) REVERT: C 736 ILE cc_start: 0.8941 (tp) cc_final: 0.8710 (tt) REVERT: C 790 ASP cc_start: 0.8930 (OUTLIER) cc_final: 0.8502 (t0) REVERT: C 916 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7992 (m-80) REVERT: D 314 CYS cc_start: 0.9279 (m) cc_final: 0.9011 (m) REVERT: D 407 MET cc_start: 0.9098 (ttp) cc_final: 0.8666 (tmm) REVERT: D 420 ASP cc_start: 0.8688 (t0) cc_final: 0.8182 (t0) REVERT: D 536 MET cc_start: 0.7759 (ptp) cc_final: 0.7551 (ptp) REVERT: D 567 TYR cc_start: 0.8431 (t80) cc_final: 0.7910 (t80) REVERT: D 571 THR cc_start: 0.8510 (p) cc_final: 0.8275 (p) outliers start: 122 outliers final: 82 residues processed: 295 average time/residue: 0.3319 time to fit residues: 158.1992 Evaluate side-chains 270 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 181 time to evaluate : 2.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 721 ASN Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 843 GLN Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 905 SER Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1063 LYS Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 770 ASP Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 793 ASN Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 916 PHE Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 1003 ASP Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 387 GLN Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 466 ARG Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 561 VAL 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: 1.9990 chunk 55 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 278 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 HIS ** B1003 ASN ** 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: 0.8251 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24452 Z= 0.190 Angle : 0.608 11.320 33409 Z= 0.299 Chirality : 0.040 0.179 3673 Planarity : 0.004 0.049 4205 Dihedral : 13.798 88.793 3712 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.15 % Allowed : 16.02 % Favored : 80.83 % 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: 1.44 (0.14), residues: 1428 sheet: -0.40 (0.29), residues: 305 loop : -1.29 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 401 HIS 0.004 0.001 HIS B1150 PHE 0.020 0.001 PHE C1117 TYR 0.016 0.001 TYR B1093 ARG 0.014 0.000 ARG B 709 *********************** 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 294 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 218 time to evaluate : 2.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.7807 (mtt) cc_final: 0.7576 (mtm) REVERT: B 471 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6912 (tmm-80) REVERT: B 518 MET cc_start: 0.9000 (mmm) cc_final: 0.8661 (mmm) REVERT: B 753 TRP cc_start: 0.9363 (OUTLIER) cc_final: 0.7705 (t60) REVERT: B 1098 MET cc_start: 0.6958 (mpp) cc_final: 0.6397 (mpp) REVERT: B 1111 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.8050 (p90) REVERT: C 396 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7485 (mtp) REVERT: C 499 GLU cc_start: 0.7777 (mp0) cc_final: 0.7500 (mp0) REVERT: C 696 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9174 (mm) REVERT: C 790 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8489 (t0) REVERT: C 916 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7926 (m-80) REVERT: D 314 CYS cc_start: 0.9163 (m) cc_final: 0.8802 (m) REVERT: D 407 MET cc_start: 0.9044 (ttp) cc_final: 0.8716 (tmm) REVERT: D 420 ASP cc_start: 0.8681 (t0) cc_final: 0.8192 (t0) REVERT: D 477 TYR cc_start: 0.9013 (p90) cc_final: 0.8772 (p90) REVERT: D 514 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7132 (mpp) REVERT: D 567 TYR cc_start: 0.8302 (t80) cc_final: 0.7777 (t80) REVERT: D 571 THR cc_start: 0.8535 (p) cc_final: 0.8326 (p) outliers start: 76 outliers final: 51 residues processed: 277 average time/residue: 0.3481 time to fit residues: 152.7074 Evaluate side-chains 252 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 193 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 905 SER Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1063 LYS Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 793 ASN Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 916 PHE Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1088 ILE Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 466 ARG Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 514 MET Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 561 VAL 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: 8.9990 chunk 31 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 chunk 157 optimal weight: 0.9990 chunk 234 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 277 optimal weight: 20.0000 chunk 173 optimal weight: 0.9980 chunk 169 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 HIS ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.5283 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= 0.236 Angle : 0.611 10.250 33409 Z= 0.298 Chirality : 0.040 0.245 3673 Planarity : 0.003 0.050 4205 Dihedral : 13.726 89.537 3712 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.27 % Allowed : 16.36 % Favored : 80.37 % 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: 0.43 (0.16), residues: 2837 helix: 1.55 (0.14), residues: 1436 sheet: -0.44 (0.29), residues: 305 loop : -1.21 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 496 HIS 0.004 0.001 HIS B1150 PHE 0.014 0.001 PHE B 289 TYR 0.020 0.001 TYR B1093 ARG 0.003 0.000 ARG B1144 *********************** 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 280 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 201 time to evaluate : 2.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.7848 (mtt) cc_final: 0.7495 (mtm) REVERT: B 402 HIS cc_start: 0.6375 (t70) cc_final: 0.5893 (t70) REVERT: B 575 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7584 (pm20) REVERT: B 753 TRP cc_start: 0.9380 (OUTLIER) cc_final: 0.7684 (t60) REVERT: B 1098 MET cc_start: 0.6804 (mpp) cc_final: 0.6250 (mpp) REVERT: B 1111 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.8008 (p90) REVERT: C 499 GLU cc_start: 0.7827 (mp0) cc_final: 0.7527 (mp0) REVERT: C 696 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9170 (mm) REVERT: C 790 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8532 (t0) REVERT: C 916 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7926 (m-80) REVERT: D 314 CYS cc_start: 0.9192 (m) cc_final: 0.8872 (m) REVERT: D 407 MET cc_start: 0.9043 (ttp) cc_final: 0.8725 (tmm) REVERT: D 420 ASP cc_start: 0.8700 (t0) cc_final: 0.8237 (t0) REVERT: D 567 TYR cc_start: 0.8348 (t80) cc_final: 0.7865 (t80) outliers start: 79 outliers final: 60 residues processed: 264 average time/residue: 0.3389 time to fit residues: 144.6312 Evaluate side-chains 256 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 190 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 905 SER Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1063 LYS Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 793 ASN Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 916 PHE Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1049 CYS Chi-restraints excluded: chain C residue 1088 ILE Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 466 ARG Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 561 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 189 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 218 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24452 Z= 0.154 Angle : 0.593 11.506 33409 Z= 0.285 Chirality : 0.039 0.244 3673 Planarity : 0.003 0.055 4205 Dihedral : 13.664 87.997 3712 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.40 % Allowed : 17.47 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.16), residues: 2837 helix: 1.74 (0.14), residues: 1435 sheet: -0.33 (0.30), residues: 301 loop : -1.07 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 496 HIS 0.004 0.001 HIS B 734 PHE 0.045 0.001 PHE C 125 TYR 0.018 0.001 TYR B1093 ARG 0.011 0.000 ARG B1041 *********************** 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 272 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 214 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.7750 (mtt) cc_final: 0.7375 (mtm) REVERT: B 582 SER cc_start: 0.9044 (m) cc_final: 0.8258 (t) REVERT: B 753 TRP cc_start: 0.9329 (OUTLIER) cc_final: 0.7621 (t60) REVERT: B 1111 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.7949 (p90) REVERT: C 1 MET cc_start: 0.6664 (tpp) cc_final: 0.6077 (tpt) REVERT: C 396 MET cc_start: 0.7533 (mtp) cc_final: 0.7332 (mtp) REVERT: C 499 GLU cc_start: 0.7702 (mp0) cc_final: 0.7396 (mp0) REVERT: C 667 MET cc_start: 0.6411 (mtm) cc_final: 0.6181 (mmm) REVERT: C 696 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9156 (mm) REVERT: C 916 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: D 100 MET cc_start: 0.8664 (mmm) cc_final: 0.8368 (mmm) REVERT: D 314 CYS cc_start: 0.9164 (m) cc_final: 0.8788 (m) REVERT: D 407 MET cc_start: 0.9010 (ttp) cc_final: 0.8687 (tmm) REVERT: D 420 ASP cc_start: 0.8700 (t0) cc_final: 0.8256 (t0) REVERT: D 477 TYR cc_start: 0.8924 (p90) cc_final: 0.8714 (p90) REVERT: D 483 MET cc_start: 0.7706 (ttp) cc_final: 0.7461 (ttp) REVERT: D 567 TYR cc_start: 0.8511 (t80) cc_final: 0.8038 (t80) outliers start: 58 outliers final: 45 residues processed: 259 average time/residue: 0.3375 time to fit residues: 141.5013 Evaluate side-chains 246 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 197 time to evaluate : 2.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 905 SER Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1063 LYS Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 793 ASN Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 916 PHE Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 466 ARG Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 561 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 10.0000 chunk 265 optimal weight: 2.9990 chunk 242 optimal weight: 0.6980 chunk 258 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 203 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 233 optimal weight: 0.0370 chunk 244 optimal weight: 10.0000 chunk 257 optimal weight: 5.9990 overall best weight: 1.1260 ------------------------------------------------------------------------------- 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 393 GLN B 402 HIS ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 GLN B 843 GLN ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 GLN ** C 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24452 Z= 0.158 Angle : 0.597 12.585 33409 Z= 0.285 Chirality : 0.039 0.187 3673 Planarity : 0.003 0.054 4205 Dihedral : 13.600 88.366 3709 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.15 % Allowed : 17.68 % Favored : 80.17 % 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: 0.80 (0.16), residues: 2837 helix: 1.86 (0.14), residues: 1434 sheet: -0.25 (0.30), residues: 301 loop : -1.06 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 496 HIS 0.014 0.001 HIS B 402 PHE 0.021 0.001 PHE B 289 TYR 0.016 0.001 TYR B1093 ARG 0.008 0.000 ARG B1041 *********************** 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 259 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 207 time to evaluate : 3.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.7753 (mtt) cc_final: 0.7366 (mtm) REVERT: B 582 SER cc_start: 0.9051 (m) cc_final: 0.8304 (t) REVERT: B 753 TRP cc_start: 0.9330 (OUTLIER) cc_final: 0.7437 (t60) REVERT: B 1096 GLN cc_start: 0.8498 (mp10) cc_final: 0.7995 (tp40) REVERT: B 1111 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.7913 (p90) REVERT: C 1 MET cc_start: 0.6894 (tpp) cc_final: 0.6331 (tpt) REVERT: C 309 ASP cc_start: 0.8203 (m-30) cc_final: 0.7895 (m-30) REVERT: C 499 GLU cc_start: 0.7693 (mp0) cc_final: 0.7388 (mp0) REVERT: C 667 MET cc_start: 0.6425 (mtm) cc_final: 0.6200 (mmm) REVERT: C 916 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7887 (m-80) REVERT: D 100 MET cc_start: 0.8604 (mmm) cc_final: 0.8345 (mmm) REVERT: D 314 CYS cc_start: 0.9154 (m) cc_final: 0.8786 (m) REVERT: D 407 MET cc_start: 0.9009 (ttp) cc_final: 0.8670 (tmm) REVERT: D 420 ASP cc_start: 0.8683 (t0) cc_final: 0.8254 (t0) REVERT: D 477 TYR cc_start: 0.8954 (p90) cc_final: 0.8727 (p90) REVERT: D 567 TYR cc_start: 0.8512 (t80) cc_final: 0.8063 (t80) REVERT: D 600 LEU cc_start: 0.8575 (mt) cc_final: 0.8355 (mt) outliers start: 52 outliers final: 44 residues processed: 246 average time/residue: 0.3364 time to fit residues: 135.4783 Evaluate side-chains 246 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 199 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 905 SER Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1063 LYS Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 793 ASN Chi-restraints excluded: chain C residue 916 PHE Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1049 CYS Chi-restraints excluded: chain C residue 1088 ILE Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 466 ARG Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 561 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 6.9990 chunk 273 optimal weight: 20.0000 chunk 166 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 190 optimal weight: 0.0270 chunk 286 optimal weight: 20.0000 chunk 264 optimal weight: 20.0000 chunk 228 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 140 optimal weight: 0.9990 overall best weight: 1.9844 ------------------------------------------------------------------------------- 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 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 944 GLN ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24452 Z= 0.186 Angle : 0.612 12.546 33409 Z= 0.292 Chirality : 0.040 0.196 3673 Planarity : 0.003 0.052 4205 Dihedral : 13.597 88.840 3709 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.15 % Allowed : 18.01 % Favored : 79.83 % 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: 0.83 (0.16), residues: 2837 helix: 1.88 (0.14), residues: 1434 sheet: -0.28 (0.30), residues: 304 loop : -1.01 (0.19), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 496 HIS 0.004 0.001 HIS B 689 PHE 0.019 0.001 PHE C 125 TYR 0.016 0.001 TYR B1093 ARG 0.008 0.000 ARG B1041 ********************** 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 257 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 205 time to evaluate : 2.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.7792 (mtt) cc_final: 0.7418 (mtm) REVERT: B 753 TRP cc_start: 0.9343 (OUTLIER) cc_final: 0.7557 (t60) REVERT: B 1111 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.7923 (p90) REVERT: C 1 MET cc_start: 0.6990 (tpp) cc_final: 0.6444 (tpt) REVERT: C 499 GLU cc_start: 0.7739 (mp0) cc_final: 0.7433 (mp0) REVERT: C 667 MET cc_start: 0.6390 (mtm) cc_final: 0.6182 (mmm) REVERT: C 790 ASP cc_start: 0.8799 (OUTLIER) cc_final: 0.8544 (t0) REVERT: C 916 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7885 (m-80) REVERT: D 100 MET cc_start: 0.8631 (mmm) cc_final: 0.8345 (mmm) REVERT: D 314 CYS cc_start: 0.9198 (m) cc_final: 0.8878 (m) REVERT: D 407 MET cc_start: 0.8977 (ttp) cc_final: 0.8634 (tmm) REVERT: D 420 ASP cc_start: 0.8716 (t0) cc_final: 0.8290 (t0) REVERT: D 477 TYR cc_start: 0.8947 (p90) cc_final: 0.8724 (p90) REVERT: D 567 TYR cc_start: 0.8542 (t80) cc_final: 0.8110 (t80) outliers start: 52 outliers final: 46 residues processed: 243 average time/residue: 0.3432 time to fit residues: 134.9246 Evaluate side-chains 246 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 196 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 905 SER Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1063 LYS Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 793 ASN Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 916 PHE Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1049 CYS Chi-restraints excluded: chain C residue 1088 ILE Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 466 ARG Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 561 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 6.9990 chunk 243 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 210 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 228 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 234 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 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 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1096 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 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 = 0.3490 r_free = 0.3490 target = 0.077346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.059512 restraints weight = 87611.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.061151 restraints weight = 50762.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.062239 restraints weight = 35136.927| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 24452 Z= 0.295 Angle : 0.661 12.387 33409 Z= 0.319 Chirality : 0.041 0.189 3673 Planarity : 0.004 0.048 4205 Dihedral : 13.671 89.722 3709 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.36 % Allowed : 18.01 % Favored : 79.63 % 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: 0.72 (0.16), residues: 2837 helix: 1.77 (0.14), residues: 1437 sheet: -0.32 (0.30), residues: 304 loop : -1.02 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 496 HIS 0.005 0.001 HIS C 984 PHE 0.018 0.001 PHE C 125 TYR 0.018 0.001 TYR B1093 ARG 0.008 0.000 ARG B1041 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4481.01 seconds wall clock time: 82 minutes 31.49 seconds (4951.49 seconds total)