Starting phenix.real_space_refine on Thu Feb 15 04:36:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h96_34556/02_2024/8h96_34556.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h96_34556/02_2024/8h96_34556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h96_34556/02_2024/8h96_34556.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h96_34556/02_2024/8h96_34556.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h96_34556/02_2024/8h96_34556.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h96_34556/02_2024/8h96_34556.pdb" } resolution = 2.78 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= 0.005 sd= 0.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 91 5.16 5 C 7057 2.51 5 N 1898 2.21 5 O 2052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 118": "OD1" <-> "OD2" Residue "A ASP 127": "OD1" <-> "OD2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A ASP 226": "OD1" <-> "OD2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A ASP 646": "OD1" <-> "OD2" Residue "A ASP 733": "OD1" <-> "OD2" Residue "A ASP 790": "OD1" <-> "OD2" Residue "A GLU 902": "OE1" <-> "OE2" Residue "B ASP 152": "OD1" <-> "OD2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B GLU 387": "OE1" <-> "OE2" Residue "B ASP 507": "OD1" <-> "OD2" Residue "B ASP 558": "OD1" <-> "OD2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 61": "OD1" <-> "OD2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C ASP 79": "OD1" <-> "OD2" 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: 11098 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7481 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 26, 'TRANS': 922} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2898 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Chain: "C" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 719 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Time building chain proxies: 6.67, per 1000 atoms: 0.60 Number of scatterers: 11098 At special positions: 0 Unit cell: (90.2, 102.3, 130.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 91 16.00 O 2052 8.00 N 1898 7.00 C 7057 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: 4.07 Conformation dependent library (CDL) restraints added in 2.0 seconds 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2672 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 12 sheets defined 41.3% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 121 through 129 removed outlier: 4.008A pdb=" N LEU A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 163 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 189 through 198 Processing helix chain 'A' and resid 201 through 211 removed outlier: 4.478A pdb=" N VAL A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR A 206 " --> pdb=" O TRP A 202 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.756A pdb=" N ASP A 226 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N SER A 227 " --> pdb=" O ASP A 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 through 227' Processing helix chain 'A' and resid 246 through 255 Processing helix chain 'A' and resid 269 through 273 removed outlier: 3.859A pdb=" N LEU A 273 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 304 removed outlier: 3.863A pdb=" N ASN A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.744A pdb=" N ASN A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 removed outlier: 3.833A pdb=" N GLN A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 346 Processing helix chain 'A' and resid 356 through 373 removed outlier: 3.513A pdb=" N THR A 370 " --> pdb=" O PHE A 366 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 401 Processing helix chain 'A' and resid 406 through 413 removed outlier: 3.814A pdb=" N TYR A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 444 through 459 removed outlier: 3.542A pdb=" N GLN A 448 " --> pdb=" O HIS A 444 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR A 456 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 removed outlier: 4.057A pdb=" N GLN A 466 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS A 467 " --> pdb=" O TRP A 464 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 468 " --> pdb=" O ASN A 465 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 463 through 468' Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 488 through 498 Processing helix chain 'A' and resid 500 through 512 removed outlier: 3.500A pdb=" N THR A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 532 removed outlier: 3.934A pdb=" N LYS A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 552 removed outlier: 3.518A pdb=" N GLU A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 562 Processing helix chain 'A' and resid 574 through 586 removed outlier: 3.859A pdb=" N LYS A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 639 removed outlier: 3.713A pdb=" N GLU A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 639 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'A' and resid 684 through 693 removed outlier: 4.069A pdb=" N PHE A 693 " --> pdb=" O TRP A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 721 Processing helix chain 'A' and resid 738 through 751 Processing helix chain 'A' and resid 766 through 779 removed outlier: 3.576A pdb=" N SER A 779 " --> pdb=" O ASN A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 807 Processing helix chain 'A' and resid 823 through 836 removed outlier: 3.752A pdb=" N ASN A 836 " --> pdb=" O GLN A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 865 removed outlier: 3.884A pdb=" N GLY A 857 " --> pdb=" O ASP A 853 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASN A 865 " --> pdb=" O MET A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 893 removed outlier: 3.689A pdb=" N LEU A 886 " --> pdb=" O GLY A 882 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 893 " --> pdb=" O GLU A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 911 No H-bonds generated for 'chain 'A' and resid 909 through 911' Processing helix chain 'A' and resid 912 through 923 Processing helix chain 'A' and resid 936 through 949 removed outlier: 3.667A pdb=" N GLY A 940 " --> pdb=" O LEU A 936 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 941 " --> pdb=" O GLY A 937 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY A 947 " --> pdb=" O THR A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 979 removed outlier: 3.832A pdb=" N CYS A 979 " --> pdb=" O LEU A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1006 Processing helix chain 'A' and resid 1018 through 1022 removed outlier: 3.712A pdb=" N GLU A1021 " --> pdb=" O TRP A1018 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR A1022 " --> pdb=" O LYS A1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1018 through 1022' Processing helix chain 'A' and resid 1023 through 1037 Processing helix chain 'A' and resid 1045 through 1049 removed outlier: 3.616A pdb=" N ALA A1048 " --> pdb=" O ASP A1045 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER A1049 " --> pdb=" O TRP A1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1045 through 1049' Processing helix chain 'B' and resid 157 through 174 removed outlier: 3.640A pdb=" N GLU B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B 169 " --> pdb=" O GLY B 165 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET B 171 " --> pdb=" O TRP B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'C' and resid 37 through 41 removed outlier: 3.545A pdb=" N GLU C 40 " --> pdb=" O PRO C 37 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 41 " --> pdb=" O ILE C 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 37 through 41' Processing helix chain 'C' and resid 51 through 58 removed outlier: 4.130A pdb=" N GLU C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG C 56 " --> pdb=" O TRP C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 73 Processing helix chain 'C' and resid 94 through 114 Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 178 removed outlier: 6.128A pdb=" N ILE A 175 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASP A 220 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE A 177 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR A 285 " --> pdb=" O ARG C 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188 Processing sheet with id=AA3, first strand: chain 'A' and resid 430 through 432 Processing sheet with id=AA4, first strand: chain 'A' and resid 568 through 571 removed outlier: 6.636A pdb=" N LEU A 674 " --> pdb=" O ASN A 702 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU A 787 " --> pdb=" O CYS A 816 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU A 844 " --> pdb=" O SER A 873 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU A 872 " --> pdb=" O GLU A 902 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU A 901 " --> pdb=" O ASP A 930 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU A 929 " --> pdb=" O GLY A 959 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU A 986 " --> pdb=" O GLY A1016 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 327 through 328 removed outlier: 5.953A pdb=" N LEU B 284 " --> pdb=" O LYS B 580 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS B 580 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LYS B 286 " --> pdb=" O HIS B 578 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N HIS B 578 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG B 288 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS B 556 " --> pdb=" O GLY B 569 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 298 through 300 removed outlier: 3.707A pdb=" N GLY B 315 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 333 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 346 through 351 removed outlier: 6.717A pdb=" N VAL B 370 " --> pdb=" O LYS B 381 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 395 through 396 removed outlier: 6.624A pdb=" N VAL B 411 " --> pdb=" O ASN B 424 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASN B 424 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE B 413 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 420 " --> pdb=" O ASP B 415 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 434 through 437 removed outlier: 3.546A pdb=" N GLY B 445 " --> pdb=" O ASN B 434 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU B 451 " --> pdb=" O GLU B 464 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU B 464 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N CYS B 453 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS B 460 " --> pdb=" O ASP B 455 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 471 through 476 removed outlier: 6.435A pdb=" N GLY B 486 " --> pdb=" O MET B 472 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU B 474 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU B 484 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N HIS B 476 " --> pdb=" O TRP B 482 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N TRP B 482 " --> pdb=" O HIS B 476 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 513 through 518 removed outlier: 6.472A pdb=" N VAL B 528 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU B 516 " --> pdb=" O ALA B 526 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA B 526 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N PHE B 518 " --> pdb=" O TRP B 524 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TRP B 524 " --> pdb=" O PHE B 518 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY B 529 " --> pdb=" O PHE B 533 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N PHE B 533 " --> pdb=" O GLY B 529 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE B 534 " --> pdb=" O GLN B 547 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN B 547 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL B 536 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 50 445 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.05 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2185 1.33 - 1.45: 2556 1.45 - 1.57: 6444 1.57 - 1.69: 0 1.69 - 1.81: 128 Bond restraints: 11313 Sorted by residual: bond pdb=" C HIS A 231 " pdb=" N ASP A 232 " ideal model delta sigma weight residual 1.334 1.520 -0.187 1.30e-02 5.92e+03 2.06e+02 bond pdb=" N VAL B 301 " pdb=" CA VAL B 301 " ideal model delta sigma weight residual 1.452 1.511 -0.058 1.18e-02 7.18e+03 2.45e+01 bond pdb=" C SER A 210 " pdb=" N GLN A 211 " ideal model delta sigma weight residual 1.331 1.234 0.097 2.07e-02 2.33e+03 2.19e+01 bond pdb=" CE1 HIS A 848 " pdb=" NE2 HIS A 848 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.55e+01 bond pdb=" N VAL B 299 " pdb=" CA VAL B 299 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.14e-02 7.69e+03 1.49e+01 ... (remaining 11308 not shown) Histogram of bond angle deviations from ideal: 89.11 - 98.12: 1 98.12 - 107.13: 293 107.13 - 116.13: 7296 116.13 - 125.14: 7512 125.14 - 134.14: 220 Bond angle restraints: 15322 Sorted by residual: angle pdb=" N LEU A 222 " pdb=" CA LEU A 222 " pdb=" CB LEU A 222 " ideal model delta sigma weight residual 110.22 89.11 21.11 1.63e+00 3.76e-01 1.68e+02 angle pdb=" N GLY A 221 " pdb=" CA GLY A 221 " pdb=" C GLY A 221 " ideal model delta sigma weight residual 113.18 131.09 -17.91 2.37e+00 1.78e-01 5.71e+01 angle pdb=" N VAL B 301 " pdb=" CA VAL B 301 " pdb=" C VAL B 301 " ideal model delta sigma weight residual 112.96 118.84 -5.88 1.00e+00 1.00e+00 3.45e+01 angle pdb=" C ASP A 853 " pdb=" CA ASP A 853 " pdb=" CB ASP A 853 " ideal model delta sigma weight residual 117.23 109.41 7.82 1.36e+00 5.41e-01 3.30e+01 angle pdb=" CA PHE B 304 " pdb=" CB PHE B 304 " pdb=" CG PHE B 304 " ideal model delta sigma weight residual 113.80 119.11 -5.31 1.00e+00 1.00e+00 2.82e+01 ... (remaining 15317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 5895 17.33 - 34.65: 716 34.65 - 51.98: 185 51.98 - 69.31: 35 69.31 - 86.64: 18 Dihedral angle restraints: 6849 sinusoidal: 2750 harmonic: 4099 Sorted by residual: dihedral pdb=" N LEU A 222 " pdb=" C LEU A 222 " pdb=" CA LEU A 222 " pdb=" CB LEU A 222 " ideal model delta harmonic sigma weight residual 122.80 95.81 26.99 0 2.50e+00 1.60e-01 1.17e+02 dihedral pdb=" C LEU A 222 " pdb=" N LEU A 222 " pdb=" CA LEU A 222 " pdb=" CB LEU A 222 " ideal model delta harmonic sigma weight residual -122.60 -111.06 -11.54 0 2.50e+00 1.60e-01 2.13e+01 dihedral pdb=" CD ARG A 843 " pdb=" NE ARG A 843 " pdb=" CZ ARG A 843 " pdb=" NH1 ARG A 843 " ideal model delta sinusoidal sigma weight residual 0.00 36.61 -36.61 1 1.00e+01 1.00e-02 1.89e+01 ... (remaining 6846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1698 0.103 - 0.206: 60 0.206 - 0.309: 5 0.309 - 0.413: 0 0.413 - 0.516: 1 Chirality restraints: 1764 Sorted by residual: chirality pdb=" CA LEU A 222 " pdb=" N LEU A 222 " pdb=" C LEU A 222 " pdb=" CB LEU A 222 " both_signs ideal model delta sigma weight residual False 2.51 3.03 -0.52 2.00e-01 2.50e+01 6.65e+00 chirality pdb=" CA ASN A 847 " pdb=" N ASN A 847 " pdb=" C ASN A 847 " pdb=" CB ASN A 847 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ILE A 851 " pdb=" N ILE A 851 " pdb=" C ILE A 851 " pdb=" CB ILE A 851 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1761 not shown) Planarity restraints: 1939 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 843 " 0.654 9.50e-02 1.11e+02 2.93e-01 5.23e+01 pdb=" NE ARG A 843 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG A 843 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 843 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 843 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 847 " -0.018 2.00e-02 2.50e+03 3.64e-02 1.33e+01 pdb=" C ASN A 847 " 0.063 2.00e-02 2.50e+03 pdb=" O ASN A 847 " -0.023 2.00e-02 2.50e+03 pdb=" N HIS A 848 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 649 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.07e+00 pdb=" C ASP A 649 " 0.043 2.00e-02 2.50e+03 pdb=" O ASP A 649 " -0.016 2.00e-02 2.50e+03 pdb=" N SER A 650 " -0.014 2.00e-02 2.50e+03 ... (remaining 1936 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1605 2.76 - 3.29: 9825 3.29 - 3.83: 16829 3.83 - 4.36: 19707 4.36 - 4.90: 36055 Nonbonded interactions: 84021 Sorted by model distance: nonbonded pdb=" N GLU B 387 " pdb=" OE1 GLU B 387 " model vdw 2.225 2.520 nonbonded pdb=" OE1 GLU A 396 " pdb=" OH TYR A 413 " model vdw 2.260 2.440 nonbonded pdb=" OG SER A 538 " pdb=" OD2 ASP A 541 " model vdw 2.279 2.440 nonbonded pdb=" O CYS A 906 " pdb=" ND2 ASN A 934 " model vdw 2.281 2.520 nonbonded pdb=" O HIS A 367 " pdb=" OG1 THR A 370 " model vdw 2.285 2.440 ... (remaining 84016 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.370 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 32.670 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 : 0.004 0.187 11313 Z= 0.257 Angle : 0.686 21.106 15322 Z= 0.407 Chirality : 0.046 0.516 1764 Planarity : 0.008 0.293 1939 Dihedral : 16.703 86.635 4177 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.52 % Allowed : 14.16 % Favored : 84.32 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.22), residues: 1395 helix: 1.41 (0.23), residues: 495 sheet: -0.39 (0.33), residues: 279 loop : -1.87 (0.22), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 525 HIS 0.004 0.001 HIS A 321 PHE 0.026 0.001 PHE B 304 TYR 0.007 0.001 TYR A 513 ARG 0.004 0.000 ARG A1027 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 1.277 Fit side-chains revert: symmetry clash REVERT: B 152 ASP cc_start: 0.3498 (OUTLIER) cc_final: 0.3041 (m-30) REVERT: B 401 MET cc_start: 0.8112 (ptp) cc_final: 0.7898 (pmm) outliers start: 19 outliers final: 12 residues processed: 127 average time/residue: 1.2195 time to fit residues: 168.0849 Evaluate side-chains 122 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 576 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS A 303 ASN A 321 HIS A 425 HIS A 431 GLN A 533 GLN A 535 ASN A 763 ASN ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN C 112 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11313 Z= 0.257 Angle : 0.584 6.602 15322 Z= 0.307 Chirality : 0.042 0.152 1764 Planarity : 0.004 0.047 1939 Dihedral : 5.577 51.934 1507 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.64 % Allowed : 14.64 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.22), residues: 1395 helix: 1.58 (0.23), residues: 499 sheet: -0.39 (0.33), residues: 287 loop : -1.97 (0.22), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 525 HIS 0.005 0.001 HIS B 292 PHE 0.020 0.002 PHE B 304 TYR 0.014 0.001 TYR B 577 ARG 0.004 0.000 ARG A1027 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 115 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 17 residues processed: 138 average time/residue: 1.1909 time to fit residues: 179.0619 Evaluate side-chains 126 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 90 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 135 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 HIS A 425 HIS A 466 GLN A 535 ASN A 763 ASN ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11313 Z= 0.275 Angle : 0.590 6.696 15322 Z= 0.309 Chirality : 0.042 0.152 1764 Planarity : 0.004 0.045 1939 Dihedral : 5.340 52.378 1496 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.20 % Allowed : 16.48 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.22), residues: 1395 helix: 1.60 (0.23), residues: 499 sheet: -0.41 (0.33), residues: 287 loop : -1.94 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 525 HIS 0.005 0.001 HIS B 578 PHE 0.024 0.002 PHE B 157 TYR 0.014 0.001 TYR B 577 ARG 0.003 0.000 ARG A1027 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 110 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 ASP cc_start: 0.5425 (OUTLIER) cc_final: 0.4959 (p0) REVERT: A 417 GLU cc_start: 0.7844 (pm20) cc_final: 0.7601 (tp30) REVERT: B 152 ASP cc_start: 0.3878 (OUTLIER) cc_final: 0.3441 (m-30) REVERT: C 61 ASP cc_start: 0.8511 (p0) cc_final: 0.8308 (p0) outliers start: 40 outliers final: 23 residues processed: 142 average time/residue: 1.1790 time to fit residues: 182.5938 Evaluate side-chains 134 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 90 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 HIS A 425 HIS A 535 ASN A 763 ASN ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11313 Z= 0.201 Angle : 0.535 7.175 15322 Z= 0.280 Chirality : 0.041 0.147 1764 Planarity : 0.004 0.045 1939 Dihedral : 5.161 51.262 1496 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.28 % Allowed : 17.76 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.23), residues: 1395 helix: 1.79 (0.23), residues: 500 sheet: -0.41 (0.33), residues: 288 loop : -1.89 (0.23), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 525 HIS 0.004 0.001 HIS A 144 PHE 0.016 0.001 PHE B 157 TYR 0.012 0.001 TYR B 577 ARG 0.006 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 111 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 PHE cc_start: 0.8196 (t80) cc_final: 0.7900 (t80) REVERT: A 186 GLU cc_start: 0.8077 (mp0) cc_final: 0.7700 (pm20) REVERT: A 200 ASP cc_start: 0.5334 (OUTLIER) cc_final: 0.4861 (p0) REVERT: A 349 ARG cc_start: 0.8105 (mpp-170) cc_final: 0.7687 (mtm-85) REVERT: A 417 GLU cc_start: 0.7847 (pm20) cc_final: 0.7556 (tp30) outliers start: 41 outliers final: 22 residues processed: 144 average time/residue: 1.1348 time to fit residues: 177.9841 Evaluate side-chains 132 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 90 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 HIS A 341 GLN A 425 HIS A 535 ASN A 763 ASN ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11313 Z= 0.421 Angle : 0.696 8.223 15322 Z= 0.361 Chirality : 0.046 0.161 1764 Planarity : 0.004 0.049 1939 Dihedral : 5.748 53.613 1496 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.68 % Allowed : 19.12 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.22), residues: 1395 helix: 1.38 (0.23), residues: 498 sheet: -0.55 (0.32), residues: 293 loop : -2.15 (0.22), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 525 HIS 0.006 0.002 HIS A 814 PHE 0.016 0.002 PHE B 157 TYR 0.016 0.002 TYR B 577 ARG 0.008 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 109 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 ASP cc_start: 0.5378 (OUTLIER) cc_final: 0.4738 (p0) REVERT: A 349 ARG cc_start: 0.8110 (mpp-170) cc_final: 0.7672 (mtm-85) REVERT: A 426 MET cc_start: 0.5980 (ttp) cc_final: 0.5778 (ttt) REVERT: C 61 ASP cc_start: 0.8462 (p0) cc_final: 0.8254 (p0) outliers start: 46 outliers final: 30 residues processed: 144 average time/residue: 1.2001 time to fit residues: 188.1928 Evaluate side-chains 135 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 104 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 733 ASP Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 90 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 128 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 HIS ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 ASN A 763 ASN ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11313 Z= 0.170 Angle : 0.529 9.332 15322 Z= 0.275 Chirality : 0.040 0.143 1764 Planarity : 0.004 0.045 1939 Dihedral : 5.172 51.393 1496 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.96 % Allowed : 20.40 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.23), residues: 1395 helix: 1.85 (0.23), residues: 499 sheet: -0.50 (0.32), residues: 288 loop : -2.00 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 525 HIS 0.003 0.001 HIS A 144 PHE 0.013 0.001 PHE B 157 TYR 0.017 0.001 TYR A 247 ARG 0.007 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 109 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 PHE cc_start: 0.8212 (t80) cc_final: 0.7937 (t80) REVERT: A 186 GLU cc_start: 0.8100 (mp0) cc_final: 0.7693 (pm20) REVERT: A 200 ASP cc_start: 0.5352 (OUTLIER) cc_final: 0.4722 (p0) REVERT: A 250 MET cc_start: 0.8116 (tpp) cc_final: 0.7850 (mmp) REVERT: A 289 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: A 417 GLU cc_start: 0.7807 (pm20) cc_final: 0.7391 (tp30) REVERT: C 61 ASP cc_start: 0.8553 (p0) cc_final: 0.8325 (p0) outliers start: 37 outliers final: 23 residues processed: 137 average time/residue: 1.1917 time to fit residues: 177.2649 Evaluate side-chains 133 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 90 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 61 optimal weight: 0.2980 chunk 82 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 HIS ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 ASN A 763 ASN ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11313 Z= 0.197 Angle : 0.541 10.201 15322 Z= 0.280 Chirality : 0.040 0.146 1764 Planarity : 0.004 0.046 1939 Dihedral : 5.124 51.079 1496 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.12 % Allowed : 20.80 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.23), residues: 1395 helix: 1.91 (0.23), residues: 499 sheet: -0.54 (0.32), residues: 288 loop : -1.98 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 525 HIS 0.004 0.001 HIS A 321 PHE 0.011 0.001 PHE A 173 TYR 0.017 0.001 TYR A 247 ARG 0.007 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 107 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8109 (mp0) cc_final: 0.7705 (pm20) REVERT: A 200 ASP cc_start: 0.5333 (OUTLIER) cc_final: 0.4686 (p0) REVERT: A 289 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7960 (mt-10) outliers start: 39 outliers final: 29 residues processed: 138 average time/residue: 1.1878 time to fit residues: 178.3720 Evaluate side-chains 136 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 105 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 90 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 7.9990 chunk 79 optimal weight: 0.0970 chunk 40 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 HIS ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 ASN A 763 ASN ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11313 Z= 0.192 Angle : 0.537 10.505 15322 Z= 0.278 Chirality : 0.040 0.145 1764 Planarity : 0.003 0.045 1939 Dihedral : 5.083 50.758 1496 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.20 % Allowed : 21.12 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.23), residues: 1395 helix: 1.96 (0.23), residues: 499 sheet: -0.54 (0.32), residues: 288 loop : -1.96 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 525 HIS 0.004 0.001 HIS A 144 PHE 0.012 0.001 PHE A 173 TYR 0.017 0.001 TYR A 247 ARG 0.006 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 107 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8112 (mp0) cc_final: 0.7711 (pm20) REVERT: A 200 ASP cc_start: 0.5292 (OUTLIER) cc_final: 0.4688 (p0) REVERT: A 250 MET cc_start: 0.8176 (tpp) cc_final: 0.7905 (mmt) REVERT: A 289 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7931 (mt-10) REVERT: A 417 GLU cc_start: 0.7827 (pm20) cc_final: 0.7337 (tp30) REVERT: A 893 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: B 401 MET cc_start: 0.7993 (ptp) cc_final: 0.7773 (pmm) REVERT: C 85 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7236 (p0) outliers start: 40 outliers final: 28 residues processed: 140 average time/residue: 1.2106 time to fit residues: 183.6667 Evaluate side-chains 139 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 107 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 90 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 3.9990 chunk 116 optimal weight: 0.4980 chunk 123 optimal weight: 0.7980 chunk 74 optimal weight: 0.0040 chunk 53 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 81 optimal weight: 0.2980 chunk 131 optimal weight: 1.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 321 HIS A 466 GLN A 535 ASN A 617 GLN A 763 ASN ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11313 Z= 0.127 Angle : 0.485 10.953 15322 Z= 0.249 Chirality : 0.038 0.150 1764 Planarity : 0.003 0.044 1939 Dihedral : 4.608 49.572 1496 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.16 % Allowed : 22.24 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.23), residues: 1395 helix: 2.26 (0.24), residues: 497 sheet: -0.48 (0.32), residues: 283 loop : -1.88 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 629 HIS 0.003 0.001 HIS A 321 PHE 0.009 0.001 PHE B 170 TYR 0.017 0.001 TYR A 247 ARG 0.005 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 PHE cc_start: 0.8187 (t80) cc_final: 0.7919 (t80) REVERT: A 186 GLU cc_start: 0.8134 (mp0) cc_final: 0.7748 (pm20) REVERT: A 200 ASP cc_start: 0.5358 (OUTLIER) cc_final: 0.4752 (p0) REVERT: A 250 MET cc_start: 0.8133 (tpp) cc_final: 0.7861 (mmt) REVERT: A 289 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: A 349 ARG cc_start: 0.7940 (mpp-170) cc_final: 0.7705 (mpp-170) REVERT: A 392 MET cc_start: 0.8119 (ttt) cc_final: 0.7884 (ttt) REVERT: A 417 GLU cc_start: 0.7770 (pm20) cc_final: 0.7293 (tp30) REVERT: A 893 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7741 (mp0) REVERT: B 401 MET cc_start: 0.7940 (ptp) cc_final: 0.7733 (pmm) REVERT: C 85 ASN cc_start: 0.7724 (OUTLIER) cc_final: 0.7171 (OUTLIER) outliers start: 27 outliers final: 12 residues processed: 141 average time/residue: 1.2308 time to fit residues: 188.6281 Evaluate side-chains 125 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 321 HIS A 535 ASN A 763 ASN ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11313 Z= 0.243 Angle : 0.592 12.020 15322 Z= 0.303 Chirality : 0.041 0.192 1764 Planarity : 0.004 0.044 1939 Dihedral : 4.969 49.320 1493 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.40 % Allowed : 22.08 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.23), residues: 1395 helix: 2.00 (0.23), residues: 499 sheet: -0.47 (0.32), residues: 288 loop : -1.92 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 167 HIS 0.005 0.001 HIS A 144 PHE 0.013 0.001 PHE A 173 TYR 0.015 0.001 TYR A 247 ARG 0.005 0.000 ARG A 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 109 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 LYS cc_start: 0.8038 (ptmt) cc_final: 0.6722 (tttm) REVERT: A 186 GLU cc_start: 0.8109 (mp0) cc_final: 0.7712 (pm20) REVERT: A 200 ASP cc_start: 0.5330 (OUTLIER) cc_final: 0.4707 (p0) REVERT: A 241 LYS cc_start: 0.8353 (mtmm) cc_final: 0.7871 (mttp) REVERT: A 250 MET cc_start: 0.8200 (tpp) cc_final: 0.7918 (mmt) REVERT: A 289 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7962 (mt-10) REVERT: A 349 ARG cc_start: 0.8071 (mpp-170) cc_final: 0.7734 (mpp-170) REVERT: A 893 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: C 85 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.7237 (OUTLIER) outliers start: 30 outliers final: 17 residues processed: 132 average time/residue: 1.2242 time to fit residues: 175.3916 Evaluate side-chains 130 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 8.9990 chunk 100 optimal weight: 0.0670 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 96 optimal weight: 0.4980 chunk 6 optimal weight: 7.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 321 HIS ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 ASN ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN C 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.173797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.139529 restraints weight = 14489.734| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.88 r_work: 0.3603 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 11313 Z= 0.239 Angle : 0.860 59.198 15322 Z= 0.496 Chirality : 0.046 0.870 1764 Planarity : 0.004 0.062 1939 Dihedral : 4.995 49.248 1493 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.00 % Allowed : 22.80 % Favored : 75.20 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.23), residues: 1395 helix: 2.00 (0.23), residues: 499 sheet: -0.48 (0.32), residues: 288 loop : -1.91 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 167 HIS 0.004 0.001 HIS A 144 PHE 0.011 0.001 PHE A 173 TYR 0.015 0.001 TYR A 247 ARG 0.004 0.000 ARG A 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3648.01 seconds wall clock time: 65 minutes 53.82 seconds (3953.82 seconds total)