Starting phenix.real_space_refine on Tue Feb 20 04:07:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krj_23004/02_2024/7krj_23004_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krj_23004/02_2024/7krj_23004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krj_23004/02_2024/7krj_23004.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krj_23004/02_2024/7krj_23004.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krj_23004/02_2024/7krj_23004_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krj_23004/02_2024/7krj_23004_trim_updated.pdb" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 74 5.16 5 C 8528 2.51 5 N 2255 2.21 5 O 2593 1.98 5 F 1 1.80 5 H 13407 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 627": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 693": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 737": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26866 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 10240 Classifications: {'peptide': 627} Link IDs: {'CIS': 4, 'PTRANS': 15, 'TRANS': 607} Chain breaks: 1 Chain: "B" Number of atoms: 10240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 10240 Classifications: {'peptide': 627} Link IDs: {'CIS': 2, 'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "C" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2122 Classifications: {'peptide': 133} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 128} Chain: "D" Number of atoms: 4172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 4172 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 243} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'DEX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.07, per 1000 atoms: 0.45 Number of scatterers: 26866 At special positions: 0 Unit cell: (136.105, 114.395, 95.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 74 16.00 P 6 15.00 Mg 2 11.99 F 1 9.00 O 2593 8.00 N 2255 7.00 C 8528 6.00 H 13407 1.00 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: 22.25 Conformation dependent library (CDL) restraints added in 2.8 seconds 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3138 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 11 sheets defined 41.8% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.47 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 42 through 64 removed outlier: 3.511A pdb=" N GLU A 47 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 49 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 70 Processing helix chain 'A' and resid 100 through 107 Processing helix chain 'A' and resid 114 through 120 Processing helix chain 'A' and resid 137 through 143 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 200 through 211 Processing helix chain 'A' and resid 301 through 303 No H-bonds generated for 'chain 'A' and resid 301 through 303' 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 430 removed outlier: 3.504A pdb=" N ILE A 412 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 413 " --> pdb=" O LYS A 410 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A 430 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 451 removed outlier: 4.901A pdb=" N SER A 442 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LYS A 443 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A 446 " --> pdb=" O LYS A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 462 removed outlier: 3.733A pdb=" N GLU A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 506 through 513 removed outlier: 5.285A pdb=" N ARG A 510 " --> pdb=" O PHE A 507 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 512 " --> pdb=" O GLU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 531 removed outlier: 4.229A pdb=" N VAL A 530 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 567 Processing helix chain 'A' and resid 569 through 578 Processing helix chain 'A' and resid 608 through 616 removed outlier: 3.954A pdb=" N ALA A 616 " --> pdb=" O ARG A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 624 No H-bonds generated for 'chain 'A' and resid 622 through 624' Processing helix chain 'A' and resid 641 through 652 Processing helix chain 'A' and resid 657 through 673 removed outlier: 3.511A pdb=" N LEU A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 695 Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'B' and resid 41 through 64 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 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 196 through 198 No H-bonds generated for 'chain 'B' and resid 196 through 198' Processing helix chain 'B' and resid 200 through 211 Processing helix chain 'B' and resid 301 through 303 No H-bonds generated for 'chain 'B' and resid 301 through 303' 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 429 removed outlier: 3.542A pdb=" N LYS B 410 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 417 " --> pdb=" O LYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 451 removed outlier: 3.619A pdb=" N GLN B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ASN B 444 " --> pdb=" O GLN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 462 removed outlier: 4.470A pdb=" N GLU B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 483 removed outlier: 3.633A pdb=" N ARG B 483 " --> pdb=" O ASP B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 503 Processing helix chain 'B' and resid 506 through 513 removed outlier: 5.266A pdb=" N ARG B 510 " --> pdb=" O PHE B 507 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG B 512 " --> pdb=" O GLU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 532 removed outlier: 4.131A pdb=" N VAL B 530 " --> pdb=" O GLU B 527 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN B 531 " --> pdb=" O TYR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 567 Processing helix chain 'B' and resid 569 through 579 Processing helix chain 'B' and resid 608 through 616 removed outlier: 3.678A pdb=" N ALA B 616 " --> pdb=" O ARG B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 624 No H-bonds generated for 'chain 'B' and resid 622 through 624' 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 695 Processing helix chain 'C' and resid 61 through 63 No H-bonds generated for 'chain 'C' and resid 61 through 63' Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 120 through 132 removed outlier: 3.544A pdb=" N GLY C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 539 Processing helix chain 'D' and resid 556 through 580 removed outlier: 3.524A pdb=" N ALA D 580 " --> pdb=" O LYS D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 586 No H-bonds generated for 'chain 'D' and resid 584 through 586' Processing helix chain 'D' and resid 589 through 615 removed outlier: 5.205A pdb=" N MET D 601 " --> pdb=" O GLN D 597 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N SER D 602 " --> pdb=" O TYR D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 655 removed outlier: 3.727A pdb=" N LEU D 647 " --> pdb=" O LYS D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 660 through 672 removed outlier: 3.748A pdb=" N LEU D 672 " --> pdb=" O THR D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 704 removed outlier: 4.326A pdb=" N ARG D 704 " --> pdb=" O ALA D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 741 removed outlier: 4.173A pdb=" N HIS D 726 " --> pdb=" O LEU D 722 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU D 727 " --> pdb=" O ASP D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 751 through 766 Proline residue: D 762 - end of helix removed outlier: 3.802A pdb=" N ASN D 766 " --> pdb=" O PRO D 762 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 284 through 289 removed outlier: 6.811A pdb=" N ILE A 78 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N PHE A 221 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU A 80 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N GLU A 223 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 325 through 331 removed outlier: 6.014A pdb=" N VAL A 365 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N PHE A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 540 through 543 Processing sheet with id= D, first strand: chain 'A' and resid 585 through 588 removed outlier: 4.413A pdb=" N LYS A 585 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 284 through 289 removed outlier: 6.921A pdb=" N ILE B 78 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N PHE B 221 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU B 80 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLU B 223 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 368 through 371 removed outlier: 6.858A pdb=" N LEU B 363 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN B 360 " --> pdb=" O ILE B 385 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 540 through 543 Processing sheet with id= H, first strand: chain 'B' and resid 585 through 588 removed outlier: 4.266A pdb=" N LYS B 585 " --> pdb=" O LYS B 632 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 99 through 101 removed outlier: 6.545A pdb=" N ALA C 6 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 28 through 32 Processing sheet with id= K, first strand: chain 'D' and resid 674 through 676 588 hydrogen bonds defined for protein. 1326 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: 10.76 Time building geometry restraints manager: 22.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 13383 1.13 - 1.30: 2456 1.30 - 1.48: 5699 1.48 - 1.65: 5445 1.65 - 1.83: 125 Bond restraints: 27108 Sorted by residual: bond pdb=" NE1 TRP C 109 " pdb=" HE1 TRP C 109 " ideal model delta sigma weight residual 0.860 1.057 -0.197 2.00e-02 2.50e+03 9.72e+01 bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.486 -0.098 1.00e-02 1.00e+04 9.69e+01 bond pdb=" C4 ATP B 801 " pdb=" C5 ATP B 801 " ideal model delta sigma weight residual 1.388 1.486 -0.098 1.00e-02 1.00e+04 9.58e+01 bond pdb=" C5 ATP B 801 " pdb=" C6 ATP B 801 " ideal model delta sigma weight residual 1.409 1.503 -0.094 1.00e-02 1.00e+04 8.87e+01 bond pdb=" NE2 GLN D 683 " pdb="HE22 GLN D 683 " ideal model delta sigma weight residual 0.860 1.047 -0.187 2.00e-02 2.50e+03 8.72e+01 ... (remaining 27103 not shown) Histogram of bond angle deviations from ideal: 73.36 - 89.66: 12 89.66 - 105.96: 576 105.96 - 122.25: 46065 122.25 - 138.55: 2419 138.55 - 154.85: 6 Bond angle restraints: 49078 Sorted by residual: angle pdb=" C ARG B 366 " pdb=" N ARG B 367 " pdb=" CA ARG B 367 " ideal model delta sigma weight residual 123.47 154.85 -31.38 1.53e+00 4.27e-01 4.21e+02 angle pdb=" C VAL B 365 " pdb=" N ARG B 366 " pdb=" CA ARG B 366 " ideal model delta sigma weight residual 122.07 148.10 -26.03 1.43e+00 4.89e-01 3.31e+02 angle pdb=" C VAL A 365 " pdb=" N ARG A 366 " pdb=" CA ARG A 366 " ideal model delta sigma weight residual 122.36 147.84 -25.48 1.42e+00 4.96e-01 3.22e+02 angle pdb=" C LEU B 107 " pdb=" N GLY B 108 " pdb=" CA GLY B 108 " ideal model delta sigma weight residual 120.79 150.63 -29.84 1.75e+00 3.27e-01 2.91e+02 angle pdb=" C VAL B 365 " pdb=" N ARG B 366 " pdb=" H ARG B 366 " ideal model delta sigma weight residual 124.11 73.36 50.76 3.00e+00 1.11e-01 2.86e+02 ... (remaining 49073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 12130 17.14 - 34.27: 363 34.27 - 51.41: 148 51.41 - 68.55: 65 68.55 - 85.69: 15 Dihedral angle restraints: 12721 sinusoidal: 7083 harmonic: 5638 Sorted by residual: dihedral pdb=" CA PRO B 348 " pdb=" C PRO B 348 " pdb=" N PHE B 349 " pdb=" CA PHE B 349 " ideal model delta harmonic sigma weight residual -180.00 -153.56 -26.44 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA PHE A 352 " pdb=" C PHE A 352 " pdb=" N GLU A 353 " pdb=" CA GLU A 353 " ideal model delta harmonic sigma weight residual 180.00 -156.53 -23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" N GLU A 25 " pdb=" C GLU A 25 " pdb=" CA GLU A 25 " pdb=" CB GLU A 25 " ideal model delta harmonic sigma weight residual 122.80 132.87 -10.07 0 2.50e+00 1.60e-01 1.62e+01 ... (remaining 12718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 1731 0.146 - 0.291: 297 0.291 - 0.437: 13 0.437 - 0.583: 2 0.583 - 0.728: 1 Chirality restraints: 2044 Sorted by residual: chirality pdb=" C8 DEX D 801 " pdb=" C14 DEX D 801 " pdb=" C7 DEX D 801 " pdb=" C9 DEX D 801 " both_signs ideal model delta sigma weight residual False 2.68 1.95 0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CB ILE B 378 " pdb=" CA ILE B 378 " pdb=" CG1 ILE B 378 " pdb=" CG2 ILE B 378 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.56 2.00e-01 2.50e+01 7.95e+00 chirality pdb=" CA GLU A 25 " pdb=" N GLU A 25 " pdb=" C GLU A 25 " pdb=" CB GLU A 25 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.54e+00 ... (remaining 2041 not shown) Planarity restraints: 3934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 350 " -0.085 2.00e-02 2.50e+03 1.62e-01 2.61e+02 pdb=" N LEU B 351 " 0.278 2.00e-02 2.50e+03 pdb=" CA LEU B 351 " -0.073 2.00e-02 2.50e+03 pdb=" H LEU B 351 " -0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 380 " -0.086 2.00e-02 2.50e+03 1.59e-01 2.53e+02 pdb=" N TYR A 381 " 0.275 2.00e-02 2.50e+03 pdb=" CA TYR A 381 " -0.076 2.00e-02 2.50e+03 pdb=" H TYR A 381 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 351 " 0.086 2.00e-02 2.50e+03 1.54e-01 2.37e+02 pdb=" N PHE B 352 " -0.266 2.00e-02 2.50e+03 pdb=" CA PHE B 352 " 0.079 2.00e-02 2.50e+03 pdb=" H PHE B 352 " 0.101 2.00e-02 2.50e+03 ... (remaining 3931 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.83: 158 1.83 - 2.53: 23210 2.53 - 3.22: 84089 3.22 - 3.91: 108087 3.91 - 4.60: 172013 Nonbonded interactions: 387557 Sorted by model distance: nonbonded pdb=" H PHE B 349 " pdb=" H ASP B 350 " model vdw 1.143 2.100 nonbonded pdb=" H TYR A 381 " pdb=" H LEU A 382 " model vdw 1.211 2.100 nonbonded pdb=" H TRP B 320 " pdb=" H GLU B 321 " model vdw 1.224 2.100 nonbonded pdb=" H GLU A 353 " pdb=" H ASN A 354 " model vdw 1.261 2.100 nonbonded pdb=" H ARG D 611 " pdb=" H SER D 612 " model vdw 1.283 2.100 ... (remaining 387552 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: 1.760 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: 0.380 Extract box with map and model: 6.930 Check model and map are aligned: 0.420 Set scattering table: 0.240 Process input model: 88.840 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.100 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:11.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 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 : 0.026 0.169 13701 Z= 1.703 Angle : 1.839 31.381 18463 Z= 1.234 Chirality : 0.107 0.728 2044 Planarity : 0.012 0.145 2341 Dihedral : 11.322 85.686 5372 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.90 % Favored : 97.98 % Rotamer: Outliers : 0.07 % Allowed : 0.27 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: 0.71 (0.20), residues: 1630 helix: 0.12 (0.17), residues: 688 sheet: 1.41 (0.30), residues: 285 loop : 0.68 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.009 TRP B 297 HIS 0.008 0.002 HIS D 775 PHE 0.036 0.005 PHE D 606 TYR 0.057 0.009 TYR D 613 ARG 0.011 0.001 ARG A 591 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.9064 (mtm) cc_final: 0.8844 (mtm) REVERT: A 628 MET cc_start: 0.7791 (mmm) cc_final: 0.7367 (mmt) REVERT: B 357 LYS cc_start: 0.7706 (tptt) cc_final: 0.7410 (tttp) REVERT: D 606 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8267 (m-10) outliers start: 1 outliers final: 1 residues processed: 205 average time/residue: 3.4472 time to fit residues: 760.1745 Evaluate side-chains 110 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain D residue 606 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN D 707 ASN D 766 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13701 Z= 0.214 Angle : 0.728 20.121 18463 Z= 0.418 Chirality : 0.043 0.173 2044 Planarity : 0.005 0.042 2341 Dihedral : 8.566 115.307 1926 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.74 % Allowed : 7.36 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: 0.81 (0.20), residues: 1630 helix: 0.64 (0.19), residues: 692 sheet: 0.93 (0.29), residues: 287 loop : 0.46 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 162 HIS 0.007 0.001 HIS D 726 PHE 0.024 0.002 PHE C 120 TYR 0.020 0.002 TYR D 735 ARG 0.006 0.001 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 MET cc_start: 0.7626 (mmm) cc_final: 0.7399 (mmm) REVERT: B 357 LYS cc_start: 0.7834 (tptt) cc_final: 0.7444 (tttp) REVERT: C 78 ARG cc_start: 0.8939 (tpt-90) cc_final: 0.8736 (tpt170) outliers start: 11 outliers final: 6 residues processed: 129 average time/residue: 3.0292 time to fit residues: 425.7235 Evaluate side-chains 104 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain D residue 606 PHE Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 678 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 147 optimal weight: 0.0470 chunk 159 optimal weight: 0.0060 chunk 131 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.1898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 707 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13701 Z= 0.196 Angle : 0.617 20.045 18463 Z= 0.356 Chirality : 0.040 0.165 2044 Planarity : 0.004 0.075 2341 Dihedral : 7.547 102.471 1926 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.80 % Allowed : 8.23 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.21), residues: 1630 helix: 0.72 (0.20), residues: 694 sheet: 0.62 (0.30), residues: 289 loop : 0.27 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 162 HIS 0.005 0.001 HIS D 726 PHE 0.014 0.001 PHE C 120 TYR 0.021 0.001 TYR D 735 ARG 0.004 0.000 ARG D 633 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 MET cc_start: 0.8458 (mtp) cc_final: 0.8227 (mtp) REVERT: B 222 VAL cc_start: 0.9103 (t) cc_final: 0.8892 (m) REVERT: B 357 LYS cc_start: 0.7872 (tptt) cc_final: 0.7526 (tttp) REVERT: C 18 GLU cc_start: 0.8611 (tt0) cc_final: 0.8287 (tm-30) REVERT: D 554 ASP cc_start: 0.6916 (p0) cc_final: 0.6216 (p0) outliers start: 12 outliers final: 6 residues processed: 116 average time/residue: 2.9434 time to fit residues: 374.1361 Evaluate side-chains 108 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 627 TYR Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain D residue 678 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 147 optimal weight: 0.0470 chunk 156 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 707 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13701 Z= 0.169 Angle : 0.584 19.872 18463 Z= 0.331 Chirality : 0.039 0.164 2044 Planarity : 0.003 0.033 2341 Dihedral : 6.994 104.768 1924 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.80 % Allowed : 8.30 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: 0.70 (0.21), residues: 1630 helix: 0.75 (0.20), residues: 695 sheet: 0.64 (0.31), residues: 277 loop : 0.26 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 557 HIS 0.005 0.001 HIS B 684 PHE 0.009 0.001 PHE A 221 TYR 0.017 0.001 TYR D 735 ARG 0.003 0.000 ARG B 612 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 MET cc_start: 0.7524 (mmm) cc_final: 0.7262 (mmm) REVERT: B 222 VAL cc_start: 0.9090 (t) cc_final: 0.8874 (m) REVERT: B 357 LYS cc_start: 0.7892 (tptt) cc_final: 0.7501 (tttp) REVERT: C 18 GLU cc_start: 0.8641 (tt0) cc_final: 0.8325 (tm-30) outliers start: 12 outliers final: 7 residues processed: 111 average time/residue: 2.7493 time to fit residues: 336.0685 Evaluate side-chains 105 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 627 TYR Chi-restraints excluded: chain D residue 704 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 140 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 707 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13701 Z= 0.223 Angle : 0.592 19.775 18463 Z= 0.335 Chirality : 0.040 0.170 2044 Planarity : 0.003 0.030 2341 Dihedral : 7.092 104.764 1924 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.60 % Allowed : 8.63 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.21), residues: 1630 helix: 0.82 (0.20), residues: 694 sheet: 0.45 (0.29), residues: 287 loop : 0.07 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 557 HIS 0.004 0.001 HIS B 684 PHE 0.012 0.001 PHE A 221 TYR 0.017 0.001 TYR D 735 ARG 0.003 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 2.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 MET cc_start: 0.8587 (mtp) cc_final: 0.8342 (mtp) REVERT: B 222 VAL cc_start: 0.9083 (t) cc_final: 0.8867 (m) REVERT: B 357 LYS cc_start: 0.7893 (tptt) cc_final: 0.7472 (tttp) REVERT: C 18 GLU cc_start: 0.8696 (tt0) cc_final: 0.8341 (tm-30) REVERT: D 585 ARG cc_start: 0.8556 (mtm110) cc_final: 0.8355 (mtm-85) outliers start: 9 outliers final: 7 residues processed: 109 average time/residue: 2.8450 time to fit residues: 341.5626 Evaluate side-chains 104 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 627 TYR Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 123 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 130 optimal weight: 0.0980 chunk 72 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 707 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13701 Z= 0.203 Angle : 0.579 19.822 18463 Z= 0.328 Chirality : 0.039 0.169 2044 Planarity : 0.003 0.030 2341 Dihedral : 6.512 83.914 1922 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.80 % Allowed : 9.04 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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 (0.21), residues: 1630 helix: 0.82 (0.20), residues: 694 sheet: 0.31 (0.29), residues: 291 loop : 0.02 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 557 HIS 0.004 0.001 HIS B 684 PHE 0.007 0.001 PHE D 774 TYR 0.016 0.001 TYR D 735 ARG 0.002 0.000 ARG B 612 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 557 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8536 (mp0) REVERT: B 180 MET cc_start: 0.8562 (mtp) cc_final: 0.8310 (mtp) REVERT: B 222 VAL cc_start: 0.9074 (t) cc_final: 0.8857 (m) REVERT: B 357 LYS cc_start: 0.7878 (tptt) cc_final: 0.7453 (tttp) REVERT: C 18 GLU cc_start: 0.8698 (tt0) cc_final: 0.8331 (tm-30) REVERT: D 585 ARG cc_start: 0.8552 (mtm110) cc_final: 0.8328 (mtm-85) outliers start: 12 outliers final: 7 residues processed: 103 average time/residue: 2.8224 time to fit residues: 324.8362 Evaluate side-chains 104 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 627 TYR Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain D residue 745 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 731 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13701 Z= 0.218 Angle : 0.581 19.714 18463 Z= 0.328 Chirality : 0.040 0.167 2044 Planarity : 0.003 0.030 2341 Dihedral : 6.504 81.495 1922 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.94 % Allowed : 9.24 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: 0.51 (0.21), residues: 1630 helix: 0.85 (0.20), residues: 692 sheet: 0.38 (0.29), residues: 287 loop : -0.07 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 557 HIS 0.004 0.001 HIS B 684 PHE 0.009 0.001 PHE A 221 TYR 0.017 0.001 TYR D 735 ARG 0.002 0.000 ARG B 612 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 557 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8558 (mp0) REVERT: B 222 VAL cc_start: 0.9068 (t) cc_final: 0.8850 (m) REVERT: B 625 MET cc_start: 0.8098 (mmt) cc_final: 0.7882 (mmt) REVERT: C 18 GLU cc_start: 0.8710 (tt0) cc_final: 0.8340 (tm-30) REVERT: C 130 MET cc_start: 0.4976 (OUTLIER) cc_final: 0.4230 (mmt) outliers start: 14 outliers final: 8 residues processed: 106 average time/residue: 2.7581 time to fit residues: 322.4889 Evaluate side-chains 104 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 627 TYR Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain D residue 745 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 0.1980 chunk 47 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 707 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13701 Z= 0.167 Angle : 0.570 19.647 18463 Z= 0.320 Chirality : 0.039 0.158 2044 Planarity : 0.003 0.062 2341 Dihedral : 6.206 76.689 1922 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.67 % Allowed : 9.50 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.21), residues: 1630 helix: 0.89 (0.20), residues: 692 sheet: 0.39 (0.29), residues: 287 loop : -0.04 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 557 HIS 0.003 0.001 HIS B 684 PHE 0.007 0.001 PHE D 774 TYR 0.015 0.001 TYR A 627 ARG 0.008 0.000 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 VAL cc_start: 0.9061 (t) cc_final: 0.8842 (m) REVERT: C 18 GLU cc_start: 0.8649 (tt0) cc_final: 0.8326 (tm-30) REVERT: D 585 ARG cc_start: 0.8499 (mtm110) cc_final: 0.8297 (mtm-85) outliers start: 10 outliers final: 8 residues processed: 101 average time/residue: 2.6763 time to fit residues: 298.7444 Evaluate side-chains 101 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 627 TYR Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain D residue 745 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 0.7980 chunk 136 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 707 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13701 Z= 0.155 Angle : 0.562 19.599 18463 Z= 0.316 Chirality : 0.039 0.153 2044 Planarity : 0.003 0.043 2341 Dihedral : 5.976 74.707 1922 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.74 % Allowed : 9.57 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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 (0.21), residues: 1630 helix: 0.98 (0.20), residues: 692 sheet: 0.41 (0.30), residues: 287 loop : 0.00 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 557 HIS 0.003 0.001 HIS B 684 PHE 0.007 0.001 PHE A 221 TYR 0.015 0.001 TYR D 735 ARG 0.008 0.000 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 557 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8545 (mp0) REVERT: B 222 VAL cc_start: 0.9070 (t) cc_final: 0.8853 (m) REVERT: C 18 GLU cc_start: 0.8627 (tt0) cc_final: 0.8321 (tm-30) outliers start: 11 outliers final: 8 residues processed: 104 average time/residue: 2.8488 time to fit residues: 325.5595 Evaluate side-chains 101 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 627 TYR Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain D residue 745 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13701 Z= 0.241 Angle : 0.591 19.574 18463 Z= 0.331 Chirality : 0.040 0.162 2044 Planarity : 0.004 0.048 2341 Dihedral : 6.366 78.739 1922 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.60 % Allowed : 10.11 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.21), residues: 1630 helix: 0.94 (0.20), residues: 692 sheet: 0.35 (0.29), residues: 287 loop : -0.09 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 557 HIS 0.005 0.001 HIS B 633 PHE 0.008 0.001 PHE A 221 TYR 0.015 0.001 TYR D 735 ARG 0.009 0.000 ARG B 201 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 557 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8541 (mp0) REVERT: B 222 VAL cc_start: 0.9050 (t) cc_final: 0.8827 (m) REVERT: C 18 GLU cc_start: 0.8672 (tt0) cc_final: 0.8360 (tm-30) outliers start: 9 outliers final: 7 residues processed: 97 average time/residue: 2.4689 time to fit residues: 267.5183 Evaluate side-chains 101 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 627 TYR Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 130 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 132 optimal weight: 0.0050 chunk 16 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.081217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.062386 restraints weight = 90944.099| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.67 r_work: 0.2986 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13701 Z= 0.150 Angle : 0.570 19.331 18463 Z= 0.319 Chirality : 0.039 0.151 2044 Planarity : 0.003 0.044 2341 Dihedral : 5.936 74.115 1922 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.60 % Allowed : 10.51 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: 0.65 (0.21), residues: 1630 helix: 1.01 (0.20), residues: 692 sheet: 0.38 (0.30), residues: 287 loop : -0.04 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 557 HIS 0.003 0.001 HIS B 684 PHE 0.007 0.001 PHE D 774 TYR 0.014 0.001 TYR D 735 ARG 0.008 0.000 ARG B 201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8652.03 seconds wall clock time: 153 minutes 3.37 seconds (9183.37 seconds total)