Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 20:41:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t2u_10369/04_2023/6t2u_10369.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t2u_10369/04_2023/6t2u_10369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t2u_10369/04_2023/6t2u_10369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t2u_10369/04_2023/6t2u_10369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t2u_10369/04_2023/6t2u_10369.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t2u_10369/04_2023/6t2u_10369.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.007 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 23826 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9047 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 51, 'TRANS': 1077} Chain breaks: 2 Chain: "C" Number of atoms: 9078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 9078 Classifications: {'peptide': 1121} Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1053} Chain: "D" Number of atoms: 4603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4603 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 25, 'TRANS': 571} Chain: "X" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1098 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain breaks: 1 Time building chain proxies: 12.53, per 1000 atoms: 0.53 Number of scatterers: 23826 At special positions: 0 Unit cell: (151.9, 151.9, 131.285, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 101 16.00 P 54 15.00 O 4582 8.00 N 4192 7.00 C 14897 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.53 Conformation dependent library (CDL) restraints added in 3.4 seconds 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5372 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 17 sheets defined 53.1% alpha, 9.1% beta 17 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 7.03 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: 3.543A pdb=" N GLU B 58 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 3.604A 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: 3.677A 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: 3.535A pdb=" N SER B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 173 removed outlier: 3.773A pdb=" N TYR B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.320A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 3.650A pdb=" N LEU B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 239 removed outlier: 3.546A 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: 3.612A pdb=" N ASN B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.683A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 317 removed outlier: 4.256A pdb=" N GLU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 3.519A pdb=" N VAL B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.643A pdb=" N MET B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 4.112A 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: 3.747A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.792A pdb=" N TYR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 461 Processing helix chain 'B' and resid 511 through 534 Processing helix chain 'B' and resid 560 through 573 Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 590 through 605 removed outlier: 3.948A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.810A 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: 3.654A pdb=" N TRP B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 668 removed outlier: 3.794A pdb=" N MET B 660 " --> pdb=" O GLY B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 677 removed outlier: 3.568A pdb=" N ASN B 673 " --> pdb=" O ASN B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 699 removed outlier: 3.608A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 717 removed outlier: 4.132A pdb=" N LEU B 707 " --> pdb=" O SER B 703 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 807 removed outlier: 3.522A pdb=" N GLU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 836 removed outlier: 4.529A pdb=" N HIS B 834 " --> pdb=" O THR B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 843 removed outlier: 3.794A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 860 removed outlier: 3.875A 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: 3.847A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1012 removed outlier: 3.686A pdb=" N GLN B1011 " --> pdb=" O SER B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 3.652A pdb=" N THR B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1048 removed outlier: 3.785A pdb=" N ALA B1048 " --> pdb=" O PRO B1045 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1045 through 1048' Processing helix chain 'B' and resid 1094 through 1106 Processing helix chain 'B' and resid 1107 through 1126 Processing helix chain 'B' and resid 1130 through 1134 Processing helix chain 'B' and resid 1144 through 1146 No H-bonds generated for 'chain 'B' and resid 1144 through 1146' Processing helix chain 'B' and resid 1163 through 1174 removed outlier: 3.595A pdb=" N LEU B1167 " --> pdb=" O GLY B1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 4.126A 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: 3.749A 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: 3.901A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 179 Proline residue: C 167 - end of helix Processing helix chain 'C' and resid 189 through 199 Processing helix chain 'C' and resid 220 through 232 removed outlier: 3.593A pdb=" N ALA C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 316 removed outlier: 3.505A pdb=" N TYR C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 344 Processing helix chain 'C' and resid 354 through 360 removed outlier: 3.522A pdb=" N ARG C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 400 removed outlier: 3.599A pdb=" N VAL C 386 " --> pdb=" O PRO C 382 " (cutoff:3.500A) removed outlier: 3.530A 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: 3.677A 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: 3.874A 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: 3.605A pdb=" N PHE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.848A pdb=" N GLN C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 removed outlier: 3.516A pdb=" N LEU C 514 " --> pdb=" O ASN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 537 Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 558 through 574 removed outlier: 3.692A pdb=" N MET C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 599 removed outlier: 4.588A pdb=" N CYS C 591 " --> pdb=" O TRP C 587 " (cutoff:3.500A) removed outlier: 4.578A 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: 3.860A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 3.901A 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 removed outlier: 3.552A pdb=" N GLN C 812 " --> pdb=" O PRO C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 843 removed outlier: 3.536A pdb=" N LEU C 837 " --> pdb=" O PRO C 833 " (cutoff:3.500A) removed outlier: 3.776A 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: 3.688A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA C 904 " --> pdb=" O ARG C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 932 removed outlier: 3.759A pdb=" N GLU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 3.863A 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: 3.606A pdb=" N GLY C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1033 removed outlier: 3.723A 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: 3.582A pdb=" N ARG C1068 " --> pdb=" O LEU C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1113 Processing helix chain 'C' and resid 1113 through 1119 removed outlier: 3.916A pdb=" N PHE C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE C1119 " --> pdb=" O PRO C1115 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.751A 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: 3.964A pdb=" N SER D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 125 Processing helix chain 'D' and resid 133 through 145 removed outlier: 3.560A pdb=" N LEU D 137 " --> pdb=" O ASP D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 164 removed outlier: 3.638A 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: 3.597A 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: 3.599A pdb=" N MET D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 286 removed outlier: 3.573A pdb=" N ALA D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 315 removed outlier: 3.789A pdb=" N ASP D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 319 removed outlier: 3.511A 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: 3.560A 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: 3.868A pdb=" N GLN D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.574A pdb=" N ALA D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 391 removed outlier: 3.599A pdb=" N THR D 391 " --> pdb=" O GLN D 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 388 through 391' Processing helix chain 'D' and resid 400 through 415 Processing helix chain 'D' and resid 415 through 424 Processing helix chain 'D' and resid 427 through 436 Processing helix chain 'D' and resid 450 through 465 Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.526A 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: 3.718A pdb=" N ILE D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 3.769A 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: 6.510A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA B 439 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 20 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLY B 17 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU B 411 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA B 381 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE B 412 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE B 383 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL B 62 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 5.660A 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: 6.252A 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: 6.519A pdb=" N VAL B 207 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 487 through 490 Processing sheet with id=AA5, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.588A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ILE B 554 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N VAL B 739 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1017 through 1027 removed outlier: 6.664A pdb=" N ASP B1067 " --> pdb=" O GLU B1020 " (cutoff:3.500A) removed outlier: 6.663A 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: 6.705A pdb=" N TYR B1024 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS B1063 " --> pdb=" O TYR B1024 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N MET B1061 " --> pdb=" O PRO B1026 " (cutoff:3.500A) removed outlier: 10.150A pdb=" N ILE B1066 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N TYR B1081 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N TYR B1076 " --> pdb=" O GLY B1137 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ILE B1139 " --> pdb=" O TYR B1076 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU B1078 " --> pdb=" O ILE B1139 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU B1141 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA B1080 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.397A pdb=" N ARG C 3 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N PHE C 240 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR C 5 " --> pdb=" O PHE C 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 265 through 266 Processing sheet with id=AA9, first strand: chain 'C' and resid 365 through 366 removed outlier: 5.977A 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: 3.556A pdb=" N ASN C 660 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LYS C 673 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N TYR C 728 " --> pdb=" O LYS C 673 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N CYS C 782 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N PHE C 376 " --> pdb=" O CYS C 782 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 442 through 443 removed outlier: 3.793A pdb=" N ARG C 442 " --> pdb=" O ILE C 650 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 939 through 947 removed outlier: 5.698A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 15.867A pdb=" N LEU C 956 " --> pdb=" O TRP C 967 " (cutoff:3.500A) removed outlier: 13.382A pdb=" N TRP C 967 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLN C 958 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU C 965 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 1050 through 1051 Processing sheet with id=AB5, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.066A pdb=" N SER D 92 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 167 through 170 removed outlier: 3.605A pdb=" N GLY D 296 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU D 266 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU D 295 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL D 268 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ARG D 200 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N SER D 238 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU D 201 " --> pdb=" O SER D 238 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 393 through 396 removed outlier: 7.397A pdb=" N ASP D 547 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLN D 439 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE D 552 " --> pdb=" O GLN D 439 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU D 441 " --> pdb=" O ILE D 552 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU D 440 " --> pdb=" O MET D 536 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 519 through 522 removed outlier: 4.460A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) 1044 hydrogen bonds defined for protein. 3066 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 9.61 Time building geometry restraints manager: 10.32 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: 7521 1.34 - 1.45: 3467 1.45 - 1.57: 13188 1.57 - 1.69: 107 1.69 - 1.81: 169 Bond restraints: 24452 Sorted by residual: bond pdb=" CD LYS D 383 " pdb=" CE LYS D 383 " ideal model delta sigma weight residual 1.520 1.580 -0.060 3.00e-02 1.11e+03 3.97e+00 bond pdb=" C THR B 304 " pdb=" N PRO B 305 " ideal model delta sigma weight residual 1.333 1.350 -0.017 1.01e-02 9.80e+03 2.74e+00 bond pdb=" N ILE B 266 " pdb=" CA ILE B 266 " ideal model delta sigma weight residual 1.474 1.458 0.016 1.57e-02 4.06e+03 1.10e+00 bond pdb=" C PRO C 823 " pdb=" N LEU C 824 " ideal model delta sigma weight residual 1.331 1.353 -0.022 2.07e-02 2.33e+03 1.09e+00 bond pdb=" CD GLN D 433 " pdb=" NE2 GLN D 433 " ideal model delta sigma weight residual 1.328 1.307 0.021 2.10e-02 2.27e+03 1.02e+00 ... (remaining 24447 not shown) Histogram of bond angle deviations from ideal: 100.01 - 106.81: 1078 106.81 - 113.61: 13083 113.61 - 120.40: 10034 120.40 - 127.20: 8869 127.20 - 134.00: 345 Bond angle restraints: 33409 Sorted by residual: angle pdb=" CG LYS D 383 " pdb=" CD LYS D 383 " pdb=" CE LYS D 383 " ideal model delta sigma weight residual 111.30 100.50 10.80 2.30e+00 1.89e-01 2.21e+01 angle pdb=" C LYS D 383 " pdb=" CA LYS D 383 " pdb=" CB LYS D 383 " ideal model delta sigma weight residual 110.67 118.66 -7.99 1.92e+00 2.71e-01 1.73e+01 angle pdb=" N GLY B 898 " pdb=" CA GLY B 898 " pdb=" C GLY B 898 " ideal model delta sigma weight residual 110.87 116.01 -5.14 1.54e+00 4.22e-01 1.12e+01 angle pdb=" N TRP B 878 " pdb=" CA TRP B 878 " pdb=" C TRP B 878 " ideal model delta sigma weight residual 107.88 112.37 -4.49 1.41e+00 5.03e-01 1.01e+01 angle pdb=" C SER C 447 " pdb=" N HIS C 448 " pdb=" CA HIS C 448 " ideal model delta sigma weight residual 119.78 123.60 -3.82 1.24e+00 6.50e-01 9.48e+00 ... (remaining 33404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 13435 16.82 - 33.64: 751 33.64 - 50.45: 302 50.45 - 67.27: 89 67.27 - 84.09: 6 Dihedral angle restraints: 14583 sinusoidal: 6294 harmonic: 8289 Sorted by residual: dihedral pdb=" C LYS D 383 " pdb=" N LYS D 383 " pdb=" CA LYS D 383 " pdb=" CB LYS D 383 " ideal model delta harmonic sigma weight residual -122.60 -134.09 11.49 0 2.50e+00 1.60e-01 2.11e+01 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 -160.75 -19.25 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLY C 657 " pdb=" C GLY C 657 " pdb=" N PRO C 658 " pdb=" CA PRO C 658 " ideal model delta harmonic sigma weight residual 180.00 163.49 16.51 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 14580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3468 0.076 - 0.151: 204 0.151 - 0.227: 0 0.227 - 0.303: 0 0.303 - 0.378: 1 Chirality restraints: 3673 Sorted by residual: chirality pdb=" CA LYS D 383 " pdb=" N LYS D 383 " pdb=" C LYS D 383 " pdb=" CB LYS D 383 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA ILE C 864 " pdb=" N ILE C 864 " pdb=" C ILE C 864 " pdb=" CB ILE C 864 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA ILE D 233 " pdb=" N ILE D 233 " pdb=" C ILE D 233 " pdb=" CB ILE D 233 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 3670 not shown) Planarity restraints: 4205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D 433 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" CD GLN D 433 " 0.057 2.00e-02 2.50e+03 pdb=" OE1 GLN D 433 " -0.021 2.00e-02 2.50e+03 pdb=" NE2 GLN D 433 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " 0.049 5.00e-02 4.00e+02 7.40e-02 8.77e+00 pdb=" N PRO C 658 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 469 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.74e+00 pdb=" C ASP C 469 " -0.048 2.00e-02 2.50e+03 pdb=" O ASP C 469 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL C 470 " 0.016 2.00e-02 2.50e+03 ... (remaining 4202 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2630 2.75 - 3.29: 21339 3.29 - 3.82: 38961 3.82 - 4.36: 44805 4.36 - 4.90: 77124 Nonbonded interactions: 184859 Sorted by model distance: nonbonded pdb=" OD1 ASN B 759 " pdb=" NH2 ARG B 822 " model vdw 2.211 2.520 nonbonded pdb=" O LEU C 115 " pdb=" OG SER C 119 " model vdw 2.283 2.440 nonbonded pdb=" O HIS B1124 " pdb=" NH2 ARG C 25 " model vdw 2.288 2.520 nonbonded pdb=" NZ LYS C 121 " pdb=" O ALA C 631 " model vdw 2.299 2.520 nonbonded pdb=" OH TYR B 394 " pdb=" OE1 GLU B 436 " model vdw 2.311 2.440 ... (remaining 184854 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.740 Check model and map are aligned: 0.380 Set scattering table: 0.210 Process input model: 66.680 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.060 24452 Z= 0.116 Angle : 0.479 10.801 33409 Z= 0.301 Chirality : 0.035 0.378 3673 Planarity : 0.005 0.074 4205 Dihedral : 13.044 84.089 9211 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.97 % Favored : 97.99 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.04 % 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: -3.59 (0.11), residues: 2837 helix: -2.51 (0.09), residues: 1400 sheet: -1.02 (0.28), residues: 301 loop : -2.39 (0.14), residues: 1136 *********************** 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 515 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 443 time to evaluate : 2.786 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 outliers start: 72 outliers final: 10 residues processed: 503 average time/residue: 0.3825 time to fit residues: 292.0656 Evaluate side-chains 205 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 195 time to evaluate : 2.802 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2708 time to fit residues: 8.4039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 8.9990 chunk 218 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 87 optimal weight: 30.0000 chunk 137 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN B 120 GLN B 134 GLN B 150 GLN B 181 GLN ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN B 417 GLN B 458 ASN B 463 GLN ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 GLN B 594 GLN B 601 GLN B 650 GLN B 700 GLN B 713 GLN B 734 HIS B 765 GLN B 769 HIS B 848 GLN ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 HIS B1084 ASN B1133 HIS B1134 HIS B1150 HIS ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS C 191 GLN C 390 HIS C 446 GLN C 510 ASN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 GLN C 660 ASN C 725 GLN C 749 GLN C 759 HIS C 817 HIS C 822 GLN C 843 HIS C 883 GLN C 925 GLN ** C 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1091 GLN C1108 GLN D 22 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN D 124 ASN D 154 GLN D 241 HIS D 251 GLN ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.144 24452 Z= 0.462 Angle : 0.821 12.525 33409 Z= 0.418 Chirality : 0.046 0.196 3673 Planarity : 0.006 0.079 4205 Dihedral : 13.390 87.986 3671 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 4.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.14), residues: 2837 helix: -0.11 (0.13), residues: 1416 sheet: -0.35 (0.29), residues: 294 loop : -1.88 (0.16), residues: 1127 *********************** 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 289 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 189 time to evaluate : 3.095 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 outliers start: 100 outliers final: 57 residues processed: 271 average time/residue: 0.3463 time to fit residues: 150.6418 Evaluate side-chains 203 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 146 time to evaluate : 2.989 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 57 outliers final: 1 residues processed: 57 average time/residue: 0.2244 time to fit residues: 27.9790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 2.9990 chunk 81 optimal weight: 30.0000 chunk 217 optimal weight: 20.0000 chunk 178 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 262 optimal weight: 10.0000 chunk 283 optimal weight: 10.0000 chunk 233 optimal weight: 0.9990 chunk 259 optimal weight: 50.0000 chunk 89 optimal weight: 30.0000 chunk 210 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN B 222 HIS B 463 GLN ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 GLN B 943 HIS ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 ASN C 126 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN D 328 GLN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 24452 Z= 0.263 Angle : 0.609 12.798 33409 Z= 0.306 Chirality : 0.040 0.193 3673 Planarity : 0.004 0.059 4205 Dihedral : 13.399 88.865 3671 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 2837 helix: 0.91 (0.13), residues: 1419 sheet: -0.16 (0.30), residues: 294 loop : -1.71 (0.17), residues: 1124 *********************** 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 216 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 166 time to evaluate : 3.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 20 residues processed: 209 average time/residue: 0.3297 time to fit residues: 113.9116 Evaluate side-chains 160 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 2.656 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2591 time to fit residues: 12.7965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 135 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 262 optimal weight: 20.0000 chunk 278 optimal weight: 20.0000 chunk 137 optimal weight: 6.9990 chunk 249 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 ASN ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 GLN ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 HIS ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 951 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 HIS D 154 GLN D 259 ASN D 463 GLN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 24452 Z= 0.354 Angle : 0.681 12.714 33409 Z= 0.347 Chirality : 0.043 0.258 3673 Planarity : 0.005 0.056 4205 Dihedral : 13.466 89.688 3671 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 2.65 % 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 (0.15), residues: 2837 helix: 0.91 (0.14), residues: 1419 sheet: -0.05 (0.31), residues: 275 loop : -1.66 (0.17), residues: 1143 *********************** 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 217 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 153 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 37 residues processed: 203 average time/residue: 0.3161 time to fit residues: 109.4778 Evaluate side-chains 174 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 137 time to evaluate : 2.920 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2189 time to fit residues: 19.1746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 4 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 237 optimal weight: 20.0000 chunk 192 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 249 optimal weight: 8.9990 chunk 70 optimal weight: 0.0470 overall best weight: 3.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 GLN ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1035 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 24452 Z= 0.247 Angle : 0.602 12.477 33409 Z= 0.303 Chirality : 0.040 0.193 3673 Planarity : 0.004 0.058 4205 Dihedral : 13.392 89.668 3671 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 1.20 % 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: 0.09 (0.16), residues: 2837 helix: 1.29 (0.14), residues: 1421 sheet: 0.03 (0.31), residues: 277 loop : -1.55 (0.17), residues: 1139 *********************** 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 178 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 149 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 13 residues processed: 173 average time/residue: 0.3399 time to fit residues: 99.6941 Evaluate side-chains 151 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 2.838 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2340 time to fit residues: 9.7290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 20.0000 chunk 250 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 163 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 278 optimal weight: 20.0000 chunk 231 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.057 24452 Z= 0.368 Angle : 0.694 13.152 33409 Z= 0.351 Chirality : 0.043 0.199 3673 Planarity : 0.005 0.057 4205 Dihedral : 13.484 89.059 3671 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 2837 helix: 0.98 (0.14), residues: 1418 sheet: 0.02 (0.31), residues: 261 loop : -1.65 (0.17), residues: 1158 *********************** 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 176 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 138 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 18 residues processed: 166 average time/residue: 0.3310 time to fit residues: 93.7246 Evaluate side-chains 153 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 2.841 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2332 time to fit residues: 11.7762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 234 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 277 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 chunk 128 optimal weight: 0.0970 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN B 531 GLN ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 HIS ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 24452 Z= 0.178 Angle : 0.571 13.916 33409 Z= 0.286 Chirality : 0.040 0.208 3673 Planarity : 0.004 0.068 4205 Dihedral : 13.385 89.560 3671 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 0.33 % 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: 0.37 (0.16), residues: 2837 helix: 1.60 (0.14), residues: 1408 sheet: 0.19 (0.32), residues: 261 loop : -1.48 (0.17), residues: 1168 *********************** 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 158 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 150 time to evaluate : 2.974 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 156 average time/residue: 0.3319 time to fit residues: 88.3115 Evaluate side-chains 148 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 143 time to evaluate : 2.848 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2443 time to fit residues: 6.3099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 83 optimal weight: 30.0000 chunk 54 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 176 optimal weight: 9.9990 chunk 189 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 218 optimal weight: 1.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 966 GLN ** B 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 HIS ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 24452 Z= 0.180 Angle : 0.574 13.015 33409 Z= 0.286 Chirality : 0.039 0.285 3673 Planarity : 0.004 0.060 4205 Dihedral : 13.353 88.126 3671 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.41 % 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: 0.56 (0.16), residues: 2837 helix: 1.77 (0.14), residues: 1409 sheet: 0.18 (0.31), residues: 272 loop : -1.41 (0.18), residues: 1156 *********************** 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 159 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 156 average time/residue: 0.3501 time to fit residues: 91.6793 Evaluate side-chains 143 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 138 time to evaluate : 2.981 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2359 time to fit residues: 6.2914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 chunk 242 optimal weight: 20.0000 chunk 258 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 203 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 233 optimal weight: 1.9990 chunk 244 optimal weight: 20.0000 chunk 257 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 985 GLN ** B1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 HIS ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 24452 Z= 0.278 Angle : 0.636 13.044 33409 Z= 0.319 Chirality : 0.041 0.266 3673 Planarity : 0.004 0.058 4205 Dihedral : 13.430 86.744 3671 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 0.66 % 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: 0.36 (0.16), residues: 2837 helix: 1.56 (0.14), residues: 1411 sheet: 0.38 (0.32), residues: 257 loop : -1.50 (0.17), residues: 1169 *********************** 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 150 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 2.912 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 146 average time/residue: 0.3601 time to fit residues: 88.6513 Evaluate side-chains 139 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 2.929 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2445 time to fit residues: 7.4654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 2.9990 chunk 273 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 190 optimal weight: 9.9990 chunk 286 optimal weight: 40.0000 chunk 264 optimal weight: 6.9990 chunk 228 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 176 optimal weight: 0.3980 chunk 140 optimal weight: 0.0060 overall best weight: 2.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 24452 Z= 0.202 Angle : 0.602 13.107 33409 Z= 0.297 Chirality : 0.040 0.254 3673 Planarity : 0.004 0.058 4205 Dihedral : 13.434 86.571 3671 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.16), residues: 2837 helix: 1.75 (0.14), residues: 1409 sheet: 0.44 (0.32), residues: 256 loop : -1.37 (0.18), residues: 1172 ********************** 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 147 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 141 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 144 average time/residue: 0.3445 time to fit residues: 82.8449 Evaluate side-chains 140 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 2.912 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2278 time to fit residues: 6.0140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 3.9990 chunk 243 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 210 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 228 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 234 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 ASN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 HIS ** 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 = 0.3888 r_free = 0.3888 target = 0.079469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.058078 restraints weight = 100958.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.059894 restraints weight = 55272.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.061079 restraints weight = 38382.105| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.6357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.057 24452 Z= 0.363 Angle : 0.711 12.957 33409 Z= 0.356 Chirality : 0.043 0.254 3673 Planarity : 0.005 0.062 4205 Dihedral : 13.588 85.566 3671 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer Outliers : 0.37 % 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: 0.06 (0.16), residues: 2837 helix: 1.23 (0.14), residues: 1409 sheet: 0.33 (0.32), residues: 247 loop : -1.53 (0.17), residues: 1181 =============================================================================== Job complete usr+sys time: 3811.06 seconds wall clock time: 70 minutes 47.40 seconds (4247.40 seconds total)