Starting phenix.real_space_refine on Sun Apr 7 18:37:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7j_23214/04_2024/7l7j_23214_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7j_23214/04_2024/7l7j_23214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7j_23214/04_2024/7l7j_23214.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7j_23214/04_2024/7l7j_23214.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7j_23214/04_2024/7l7j_23214_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7j_23214/04_2024/7l7j_23214_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.068 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 6 5.49 5 S 52 5.16 5 C 7082 2.51 5 N 1897 2.21 5 O 2159 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 13": "OD1" <-> "OD2" Residue "C TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 54": "OD1" <-> "OD2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 93": "OD1" <-> "OD2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 553": "OE1" <-> "OE2" Residue "A PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 621": "OD1" <-> "OD2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 25": "OE1" <-> "OE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 401": "OE1" <-> "OE2" Residue "B PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 580": "OE1" <-> "OE2" Residue "B TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 651": "OE1" <-> "OE2" Residue "B PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11196 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 920 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "A" Number of atoms: 5107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 5107 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 15, 'TRANS': 612} Chain breaks: 1 Chain: "B" Number of atoms: 5107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 5107 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 15, 'TRANS': 612} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.39, per 1000 atoms: 0.57 Number of scatterers: 11196 At special positions: 0 Unit cell: (96.866, 98.494, 130.24, 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 52 16.00 P 6 15.00 O 2159 8.00 N 1897 7.00 C 7082 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: 3.84 Conformation dependent library (CDL) restraints added in 1.5 seconds 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2608 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 11 sheets defined 38.1% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 removed outlier: 3.604A pdb=" N SER A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 65 removed outlier: 3.522A pdb=" N LEU A 45 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 47 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 48 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN A 51 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP A 54 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 56 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A 58 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 60 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 65 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 70 Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 406 through 429 removed outlier: 3.526A pdb=" N ASN A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU A 429 " --> pdb=" O THR A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 451 removed outlier: 4.616A pdb=" N GLN A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ASN A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 462 removed outlier: 4.188A pdb=" N GLU A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 483 Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 506 through 513 removed outlier: 4.872A pdb=" N ARG A 510 " --> pdb=" O PHE A 507 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 512 " --> pdb=" O GLU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.550A pdb=" N CYS A 529 " --> pdb=" O ASP A 526 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL A 530 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 578 removed outlier: 5.763A pdb=" N ASN A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 616 removed outlier: 3.637A pdb=" N ALA A 616 " --> pdb=" O ARG A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 628 removed outlier: 3.604A pdb=" N TYR A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N MET A 628 " --> pdb=" O THR A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 652 Processing helix chain 'A' and resid 657 through 673 Processing helix chain 'A' and resid 681 through 696 removed outlier: 4.104A pdb=" N ARG A 687 " --> pdb=" O THR A 683 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 688 " --> pdb=" O HIS A 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 35 Processing helix chain 'B' and resid 41 through 64 removed outlier: 3.553A pdb=" N LEU B 48 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE B 49 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 51 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 56 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS B 58 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 60 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR B 61 " --> pdb=" O LYS B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 70 Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.975A pdb=" N ALA B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 192 through 198 removed outlier: 3.882A pdb=" N THR B 195 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLU B 196 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 211 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 306 through 317 Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 406 through 427 removed outlier: 3.666A pdb=" N LYS B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 451 removed outlier: 4.367A pdb=" N GLN B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ASN B 444 " --> pdb=" O GLN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 462 removed outlier: 3.681A pdb=" N GLU B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 483 Processing helix chain 'B' and resid 499 through 503 Processing helix chain 'B' and resid 506 through 513 removed outlier: 4.882A pdb=" N ARG B 510 " --> pdb=" O PHE B 507 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG B 512 " --> pdb=" O GLU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 530 removed outlier: 3.691A pdb=" N VAL B 530 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 567 Processing helix chain 'B' and resid 569 through 578 Processing helix chain 'B' and resid 608 through 616 Processing helix chain 'B' and resid 622 through 628 removed outlier: 3.599A pdb=" N GLY B 626 " --> pdb=" O ASN B 622 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR B 627 " --> pdb=" O SER B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 652 Processing helix chain 'B' and resid 657 through 673 Processing helix chain 'B' and resid 681 through 696 removed outlier: 3.658A pdb=" N ARG B 687 " --> pdb=" O THR B 683 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 99 through 101 removed outlier: 6.516A pdb=" N ALA C 6 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 28 through 32 Processing sheet with id= C, first strand: chain 'A' and resid 171 through 174 removed outlier: 7.055A pdb=" N HIS A 189 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL A 148 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A 187 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL A 150 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LYS A 185 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR A 152 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLY A 183 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 88 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU A 80 " --> pdb=" O PRO A 217 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR A 219 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE A 221 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 325 through 331 removed outlier: 3.777A pdb=" N ALA A 325 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL A 365 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N PHE A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 540 through 543 removed outlier: 6.052A pdb=" N ILE A 519 " --> pdb=" O ILE A 494 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 585 through 589 removed outlier: 4.009A pdb=" N LYS A 585 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 218 through 221 removed outlier: 6.513A pdb=" N ILE B 78 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N PHE B 221 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU B 80 " --> pdb=" O PHE B 221 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 368 through 371 removed outlier: 6.980A pdb=" N LEU B 363 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLY B 387 " --> pdb=" O LYS B 362 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N TYR B 364 " --> pdb=" O GLY B 387 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL B 389 " --> pdb=" O TYR B 364 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 325 " --> pdb=" O VAL B 343 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 464 through 466 Processing sheet with id= J, first strand: chain 'B' and resid 540 through 543 removed outlier: 6.074A pdb=" N ILE B 519 " --> pdb=" O ILE B 494 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 585 through 588 removed outlier: 3.982A pdb=" N LYS B 585 " --> pdb=" O LYS B 632 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1083 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: 3.48 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1967 1.31 - 1.43: 2776 1.43 - 1.56: 6552 1.56 - 1.69: 8 1.69 - 1.82: 87 Bond restraints: 11390 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.535 0.165 2.00e-02 2.50e+03 6.83e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.536 0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" O5' ANP B 801 " pdb=" PA ANP B 801 " ideal model delta sigma weight residual 1.655 1.543 0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" O5' ANP A 801 " pdb=" PA ANP A 801 " ideal model delta sigma weight residual 1.655 1.551 0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.60e+01 ... (remaining 11385 not shown) Histogram of bond angle deviations from ideal: 98.67 - 106.08: 250 106.08 - 113.48: 5886 113.48 - 120.88: 5739 120.88 - 128.28: 3401 128.28 - 135.69: 49 Bond angle restraints: 15325 Sorted by residual: angle pdb=" CA ASP B 286 " pdb=" CB ASP B 286 " pdb=" CG ASP B 286 " ideal model delta sigma weight residual 112.60 118.93 -6.33 1.00e+00 1.00e+00 4.00e+01 angle pdb=" CA PHE A 221 " pdb=" CB PHE A 221 " pdb=" CG PHE A 221 " ideal model delta sigma weight residual 113.80 120.07 -6.27 1.00e+00 1.00e+00 3.93e+01 angle pdb=" CA ASP A 322 " pdb=" CB ASP A 322 " pdb=" CG ASP A 322 " ideal model delta sigma weight residual 112.60 118.52 -5.92 1.00e+00 1.00e+00 3.50e+01 angle pdb=" N ARG B 591 " pdb=" CA ARG B 591 " pdb=" C ARG B 591 " ideal model delta sigma weight residual 113.16 120.45 -7.29 1.24e+00 6.50e-01 3.45e+01 angle pdb=" CA ASN B 622 " pdb=" CB ASN B 622 " pdb=" CG ASN B 622 " ideal model delta sigma weight residual 112.60 118.14 -5.54 1.00e+00 1.00e+00 3.07e+01 ... (remaining 15320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.41: 6867 31.41 - 62.81: 141 62.81 - 94.22: 32 94.22 - 125.63: 0 125.63 - 157.03: 2 Dihedral angle restraints: 7042 sinusoidal: 3021 harmonic: 4021 Sorted by residual: dihedral pdb=" CA GLU A 392 " pdb=" C GLU A 392 " pdb=" N ASP A 393 " pdb=" CA ASP A 393 " ideal model delta harmonic sigma weight residual 180.00 -151.14 -28.86 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASP B 286 " pdb=" C ASP B 286 " pdb=" N GLN B 287 " pdb=" CA GLN B 287 " ideal model delta harmonic sigma weight residual 180.00 151.45 28.55 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA MET A 521 " pdb=" C MET A 521 " pdb=" N ILE A 522 " pdb=" CA ILE A 522 " ideal model delta harmonic sigma weight residual -180.00 -153.45 -26.55 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 7039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 984 0.070 - 0.139: 519 0.139 - 0.209: 154 0.209 - 0.278: 22 0.278 - 0.348: 14 Chirality restraints: 1693 Sorted by residual: chirality pdb=" CA PHE A 329 " pdb=" N PHE A 329 " pdb=" C PHE A 329 " pdb=" CB PHE A 329 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA ALA A 111 " pdb=" N ALA A 111 " pdb=" C ALA A 111 " pdb=" CB ALA A 111 " both_signs ideal model delta sigma weight residual False 2.48 2.15 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA ARG A 367 " pdb=" N ARG A 367 " pdb=" C ARG A 367 " pdb=" CB ARG A 367 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 1690 not shown) Planarity restraints: 1946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 297 " 0.081 2.00e-02 2.50e+03 6.09e-02 9.27e+01 pdb=" CG TRP A 297 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP A 297 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 297 " -0.043 2.00e-02 2.50e+03 pdb=" NE1 TRP A 297 " -0.088 2.00e-02 2.50e+03 pdb=" CE2 TRP A 297 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP A 297 " -0.080 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 297 " 0.080 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 297 " -0.039 2.00e-02 2.50e+03 pdb=" CH2 TRP A 297 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 309 " 0.120 2.00e-02 2.50e+03 6.30e-02 7.94e+01 pdb=" CG TYR A 309 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR A 309 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TYR A 309 " -0.053 2.00e-02 2.50e+03 pdb=" CE1 TYR A 309 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR A 309 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR A 309 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 309 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 109 " 0.110 2.00e-02 2.50e+03 5.47e-02 7.49e+01 pdb=" CG TRP C 109 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP C 109 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP C 109 " -0.053 2.00e-02 2.50e+03 pdb=" NE1 TRP C 109 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP C 109 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP C 109 " -0.082 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 109 " 0.051 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 109 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 109 " 0.061 2.00e-02 2.50e+03 ... (remaining 1943 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 4273 2.92 - 3.42: 10787 3.42 - 3.91: 19403 3.91 - 4.41: 22041 4.41 - 4.90: 37228 Nonbonded interactions: 93732 Sorted by model distance: nonbonded pdb=" ND2 ASN B 51 " pdb=" O1A ANP B 801 " model vdw 2.427 2.520 nonbonded pdb=" N GLU A 200 " pdb=" OE1 GLU A 200 " model vdw 2.505 2.520 nonbonded pdb=" ND2 ASN A 51 " pdb=" O1A ANP A 801 " model vdw 2.526 2.520 nonbonded pdb=" OG SER B 589 " pdb=" OE1 GLU B 635 " model vdw 2.552 2.440 nonbonded pdb=" OD1 ASP B 57 " pdb=" OH TYR B 216 " model vdw 2.564 2.440 ... (remaining 93727 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.160 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: 10.800 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 31.160 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 : 0.012 0.165 11390 Z= 0.775 Angle : 1.770 14.121 15325 Z= 1.164 Chirality : 0.090 0.348 1693 Planarity : 0.012 0.103 1946 Dihedral : 14.104 157.032 4434 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.28 % Favored : 95.58 % Rotamer: Outliers : 0.73 % Allowed : 3.14 % Favored : 96.13 % Cbeta Deviations : 0.08 % 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: -1.39 (0.21), residues: 1356 helix: -1.76 (0.18), residues: 488 sheet: 0.22 (0.34), residues: 232 loop : -0.49 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.110 0.022 TRP C 109 HIS 0.016 0.004 HIS A 633 PHE 0.082 0.014 PHE A 507 TYR 0.120 0.021 TYR A 309 ARG 0.008 0.001 ARG A 687 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 200 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 THR cc_start: 0.8047 (p) cc_final: 0.7722 (m) REVERT: B 498 THR cc_start: 0.8030 (p) cc_final: 0.7698 (m) outliers start: 9 outliers final: 2 residues processed: 206 average time/residue: 0.3327 time to fit residues: 90.1219 Evaluate side-chains 107 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain B residue 591 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN A 633 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11390 Z= 0.217 Angle : 0.565 7.249 15325 Z= 0.309 Chirality : 0.042 0.175 1693 Planarity : 0.003 0.026 1946 Dihedral : 8.182 143.774 1547 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.45 % Allowed : 7.90 % Favored : 90.65 % 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: 0.22 (0.22), residues: 1356 helix: 0.27 (0.22), residues: 482 sheet: 0.23 (0.33), residues: 251 loop : 0.20 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 162 HIS 0.005 0.001 HIS B 189 PHE 0.026 0.001 PHE C 103 TYR 0.017 0.002 TYR A 381 ARG 0.004 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.7755 (t0) cc_final: 0.7437 (t0) REVERT: A 614 MET cc_start: 0.7577 (mmm) cc_final: 0.6639 (mmm) REVERT: B 498 THR cc_start: 0.8190 (p) cc_final: 0.7725 (m) outliers start: 18 outliers final: 10 residues processed: 136 average time/residue: 0.2740 time to fit residues: 51.6155 Evaluate side-chains 106 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 636 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 109 optimal weight: 0.1980 chunk 121 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11390 Z= 0.197 Angle : 0.502 5.579 15325 Z= 0.274 Chirality : 0.041 0.147 1693 Planarity : 0.003 0.034 1946 Dihedral : 7.613 135.705 1542 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.05 % Allowed : 8.78 % Favored : 90.17 % 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: 0.53 (0.23), residues: 1356 helix: 0.91 (0.23), residues: 484 sheet: 0.16 (0.32), residues: 256 loop : 0.15 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 162 HIS 0.004 0.001 HIS B 189 PHE 0.011 0.001 PHE C 103 TYR 0.015 0.002 TYR A 381 ARG 0.017 0.001 ARG A 620 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.7725 (t0) cc_final: 0.7461 (t0) REVERT: A 208 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7860 (ttpt) REVERT: B 498 THR cc_start: 0.8019 (p) cc_final: 0.7814 (m) REVERT: B 610 MET cc_start: 0.7854 (tpt) cc_final: 0.7521 (tpt) outliers start: 13 outliers final: 8 residues processed: 126 average time/residue: 0.2676 time to fit residues: 47.8520 Evaluate side-chains 109 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 628 MET Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 669 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 64 optimal weight: 0.0270 chunk 116 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11390 Z= 0.192 Angle : 0.482 7.028 15325 Z= 0.261 Chirality : 0.040 0.150 1693 Planarity : 0.003 0.037 1946 Dihedral : 7.348 132.948 1542 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.21 % Allowed : 9.51 % Favored : 89.28 % 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: 0.68 (0.23), residues: 1356 helix: 1.17 (0.23), residues: 484 sheet: 0.19 (0.32), residues: 252 loop : 0.11 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 162 HIS 0.004 0.001 HIS B 189 PHE 0.012 0.001 PHE C 103 TYR 0.014 0.001 TYR B 434 ARG 0.005 0.000 ARG B 620 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 116 average time/residue: 0.2664 time to fit residues: 44.1644 Evaluate side-chains 106 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 669 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 HIS A 633 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11390 Z= 0.267 Angle : 0.505 8.196 15325 Z= 0.271 Chirality : 0.041 0.153 1693 Planarity : 0.003 0.037 1946 Dihedral : 7.350 134.998 1542 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.13 % Allowed : 10.39 % Favored : 88.48 % 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: 0.63 (0.23), residues: 1356 helix: 1.17 (0.23), residues: 484 sheet: -0.04 (0.31), residues: 262 loop : 0.16 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 162 HIS 0.015 0.001 HIS A 633 PHE 0.013 0.001 PHE C 103 TYR 0.017 0.002 TYR B 139 ARG 0.004 0.000 ARG B 620 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 610 MET cc_start: 0.8076 (tpt) cc_final: 0.7651 (tpt) outliers start: 14 outliers final: 11 residues processed: 113 average time/residue: 0.2483 time to fit residues: 40.6994 Evaluate side-chains 98 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 669 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11390 Z= 0.221 Angle : 0.475 8.690 15325 Z= 0.256 Chirality : 0.040 0.148 1693 Planarity : 0.003 0.037 1946 Dihedral : 7.162 132.208 1542 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.21 % Allowed : 10.72 % Favored : 88.07 % 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: 0.66 (0.23), residues: 1356 helix: 1.25 (0.23), residues: 484 sheet: -0.06 (0.31), residues: 262 loop : 0.14 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 162 HIS 0.004 0.001 HIS B 189 PHE 0.013 0.001 PHE C 103 TYR 0.015 0.002 TYR B 434 ARG 0.003 0.000 ARG B 620 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 393 ASP cc_start: 0.7067 (t70) cc_final: 0.6776 (t70) REVERT: B 610 MET cc_start: 0.8130 (tpt) cc_final: 0.7683 (tpt) outliers start: 15 outliers final: 10 residues processed: 106 average time/residue: 0.2643 time to fit residues: 39.8298 Evaluate side-chains 96 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 669 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11390 Z= 0.262 Angle : 0.498 8.213 15325 Z= 0.265 Chirality : 0.041 0.150 1693 Planarity : 0.003 0.035 1946 Dihedral : 7.199 134.701 1542 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.21 % Allowed : 10.96 % Favored : 87.83 % 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: 0.50 (0.23), residues: 1356 helix: 1.16 (0.23), residues: 488 sheet: -0.16 (0.31), residues: 263 loop : 0.01 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 162 HIS 0.004 0.001 HIS B 189 PHE 0.010 0.001 PHE B 337 TYR 0.016 0.002 TYR B 434 ARG 0.002 0.000 ARG B 591 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 393 ASP cc_start: 0.7171 (t70) cc_final: 0.6904 (t70) outliers start: 15 outliers final: 11 residues processed: 108 average time/residue: 0.2632 time to fit residues: 40.5416 Evaluate side-chains 103 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 669 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11390 Z= 0.261 Angle : 0.498 7.860 15325 Z= 0.265 Chirality : 0.041 0.151 1693 Planarity : 0.003 0.037 1946 Dihedral : 7.186 134.823 1542 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.29 % Allowed : 11.85 % Favored : 86.87 % 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 (0.23), residues: 1356 helix: 1.18 (0.23), residues: 488 sheet: -0.20 (0.31), residues: 263 loop : -0.01 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 162 HIS 0.004 0.001 HIS B 189 PHE 0.010 0.001 PHE B 337 TYR 0.016 0.002 TYR B 434 ARG 0.005 0.000 ARG A 620 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 393 ASP cc_start: 0.7161 (t70) cc_final: 0.6891 (t70) REVERT: B 610 MET cc_start: 0.8107 (tpt) cc_final: 0.7676 (tpt) outliers start: 16 outliers final: 14 residues processed: 109 average time/residue: 0.2387 time to fit residues: 37.4932 Evaluate side-chains 98 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 669 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 124 optimal weight: 0.0670 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11390 Z= 0.227 Angle : 0.478 7.789 15325 Z= 0.256 Chirality : 0.040 0.147 1693 Planarity : 0.003 0.038 1946 Dihedral : 7.078 133.470 1542 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.13 % Allowed : 12.25 % Favored : 86.62 % 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: 0.53 (0.23), residues: 1356 helix: 1.24 (0.23), residues: 488 sheet: -0.07 (0.31), residues: 257 loop : -0.07 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 162 HIS 0.004 0.001 HIS B 189 PHE 0.009 0.001 PHE B 337 TYR 0.016 0.002 TYR B 434 ARG 0.002 0.000 ARG B 591 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 393 ASP cc_start: 0.7118 (t70) cc_final: 0.6839 (t70) REVERT: B 610 MET cc_start: 0.8115 (tpt) cc_final: 0.7689 (tpt) outliers start: 14 outliers final: 13 residues processed: 116 average time/residue: 0.2626 time to fit residues: 43.2858 Evaluate side-chains 102 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 669 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11390 Z= 0.227 Angle : 0.487 7.701 15325 Z= 0.260 Chirality : 0.041 0.147 1693 Planarity : 0.003 0.037 1946 Dihedral : 7.071 133.621 1542 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.97 % Allowed : 12.65 % Favored : 86.38 % 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: 0.60 (0.23), residues: 1356 helix: 1.30 (0.24), residues: 484 sheet: -0.09 (0.31), residues: 257 loop : 0.01 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 162 HIS 0.004 0.001 HIS B 189 PHE 0.009 0.001 PHE B 337 TYR 0.015 0.002 TYR B 434 ARG 0.002 0.000 ARG B 591 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 393 ASP cc_start: 0.7083 (t70) cc_final: 0.6834 (t70) REVERT: B 610 MET cc_start: 0.8098 (tpt) cc_final: 0.7657 (tpt) outliers start: 12 outliers final: 12 residues processed: 104 average time/residue: 0.2321 time to fit residues: 35.8809 Evaluate side-chains 103 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 669 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 19 optimal weight: 0.0470 chunk 94 optimal weight: 0.5980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.129339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.097025 restraints weight = 16092.962| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.77 r_work: 0.3165 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11390 Z= 0.152 Angle : 0.450 7.879 15325 Z= 0.243 Chirality : 0.040 0.145 1693 Planarity : 0.003 0.038 1946 Dihedral : 6.763 128.051 1542 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.73 % Allowed : 12.73 % Favored : 86.54 % 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: 0.79 (0.23), residues: 1356 helix: 1.57 (0.24), residues: 480 sheet: -0.06 (0.31), residues: 262 loop : 0.07 (0.27), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 162 HIS 0.003 0.001 HIS A 323 PHE 0.008 0.001 PHE C 103 TYR 0.014 0.001 TYR B 434 ARG 0.002 0.000 ARG B 591 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2345.72 seconds wall clock time: 43 minutes 49.02 seconds (2629.02 seconds total)