Starting phenix.real_space_refine on Wed Jul 24 19:53:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krj_23004/07_2024/7krj_23004_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krj_23004/07_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_23004/07_2024/7krj_23004.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krj_23004/07_2024/7krj_23004.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krj_23004/07_2024/7krj_23004_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krj_23004/07_2024/7krj_23004_neut_trim.cif" } 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-5388/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: 12.76, per 1000 atoms: 0.47 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: 22.93 Conformation dependent library (CDL) restraints added in 2.6 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... Secondary structure from input PDB file: 67 helices and 13 sheets defined 46.9% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 42 through 63 removed outlier: 3.712A pdb=" N ARG A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 65 No H-bonds generated for 'chain 'A' and resid 64 through 65' Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 113 through 121 Processing helix chain 'A' and resid 136 through 144 Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 199 through 212 removed outlier: 3.940A pdb=" N GLN A 212 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 304 Processing helix chain 'A' and resid 305 through 318 Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 407 through 431 removed outlier: 3.927A pdb=" N VAL A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 452 removed outlier: 6.459A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ASN A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 461 removed outlier: 3.733A pdb=" N GLU A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 498 through 504 Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 508 through 514 Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 554 through 568 Processing helix chain 'A' and resid 568 through 579 Processing helix chain 'A' and resid 607 through 615 Processing helix chain 'A' and resid 621 through 625 Processing helix chain 'A' and resid 640 through 653 Processing helix chain 'A' and resid 656 through 674 removed outlier: 3.511A pdb=" N LEU A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 696 removed outlier: 4.057A pdb=" N HIS A 684 " --> pdb=" O ASP A 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 37 removed outlier: 3.802A pdb=" N PHE B 37 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 43 through 63 Processing helix chain 'B' and resid 64 through 65 No H-bonds generated for 'chain 'B' and resid 64 through 65' Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.564A pdb=" N GLY B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 122 Processing helix chain 'B' and resid 137 through 143 Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 199 through 212 removed outlier: 4.191A pdb=" N GLN B 212 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 305 through 318 Processing helix chain 'B' and resid 379 through 383 Processing helix chain 'B' and resid 406 through 428 removed outlier: 3.583A pdb=" N LYS B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 411 " --> pdb=" O LYS B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 452 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 455 through 460 Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 476 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 498 through 504 Processing helix chain 'B' and resid 505 through 507 No H-bonds generated for 'chain 'B' and resid 505 through 507' Processing helix chain 'B' and resid 508 through 514 Processing helix chain 'B' and resid 525 through 531 removed outlier: 3.834A pdb=" N GLN B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 568 Processing helix chain 'B' and resid 568 through 580 Processing helix chain 'B' and resid 607 through 615 Processing helix chain 'B' and resid 621 through 625 Processing helix chain 'B' and resid 640 through 653 Processing helix chain 'B' and resid 656 through 674 Processing helix chain 'B' and resid 680 through 696 removed outlier: 3.673A pdb=" N HIS B 684 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 106 Processing helix chain 'C' and resid 119 through 131 Processing helix chain 'D' and resid 531 through 540 Processing helix chain 'D' and resid 555 through 581 removed outlier: 3.524A pdb=" N ALA D 580 " --> pdb=" O LYS D 576 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE D 581 " --> pdb=" O TRP D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 587 Processing helix chain 'D' and resid 588 through 614 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 656 Processing helix chain 'D' and resid 659 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 682 through 703 Processing helix chain 'D' and resid 707 through 742 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 750 through 765 Proline residue: D 762 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21 removed outlier: 6.008A pdb=" N GLU B 223 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 284 through 289 removed outlier: 6.313A pdb=" N GLU A 223 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA4, 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=AA5, first strand: chain 'A' and resid 466 through 467 removed outlier: 4.222A pdb=" N TYR A 466 " --> pdb=" O TYR A 520 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE A 491 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 586 through 588 removed outlier: 7.034A pdb=" N VAL A 587 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 323 through 331 removed outlier: 6.598A pdb=" N VAL B 343 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL B 326 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU B 341 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HIS B 328 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA B 339 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER B 330 " --> pdb=" O PHE B 337 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE B 337 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU B 363 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 466 through 467 removed outlier: 4.212A pdb=" N TYR B 466 " --> pdb=" O TYR B 520 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE B 491 " --> pdb=" O VAL B 542 " (cutoff:3.500A) Processing sheet with id=AA9, 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=AB1, first strand: chain 'C' and resid 59 through 68 removed outlier: 6.847A pdb=" N ASP C 63 " --> pdb=" O ARG C 78 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG C 78 " --> pdb=" O ASP C 63 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 24 through 32 removed outlier: 4.552A pdb=" N VAL C 27 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER C 39 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL C 29 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR C 37 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N PHE C 31 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS C 35 " --> pdb=" O PHE C 31 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 621 through 622 Processing sheet with id=AB4, first strand: chain 'D' and resid 674 through 676 667 hydrogen bonds defined for protein. 1833 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: 10.48 Time building geometry restraints manager: 24.00 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: 150 1.83 - 2.53: 23050 2.53 - 3.22: 84067 3.22 - 3.91: 108107 3.91 - 4.60: 171788 Nonbonded interactions: 387162 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 387157 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: 1.430 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: 0.900 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 87.350 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.830 ------------------------------------------------------------------------------- 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= 1.713 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 : 2.104 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: 3.3955 time to fit residues: 749.0547 Evaluate side-chains 110 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 2.002 ------------------------------------------------------------------------------- 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: 7.9990 chunk 122 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 707 ASN D 766 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13701 Z= 0.210 Angle : 0.740 20.071 18463 Z= 0.421 Chirality : 0.042 0.179 2044 Planarity : 0.004 0.042 2341 Dihedral : 8.649 116.256 1926 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.94 % Allowed : 7.16 % 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: 1.09 (0.20), residues: 1630 helix: 1.03 (0.19), residues: 700 sheet: 0.86 (0.29), residues: 294 loop : 0.52 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 162 HIS 0.006 0.001 HIS D 726 PHE 0.020 0.002 PHE C 120 TYR 0.021 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 136 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 2.195 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 180 MET cc_start: 0.8504 (mtp) cc_final: 0.8247 (mtp) REVERT: B 357 LYS cc_start: 0.7843 (tptt) cc_final: 0.7461 (tttp) REVERT: C 78 ARG cc_start: 0.8944 (tpt-90) cc_final: 0.8742 (tpt170) outliers start: 14 outliers final: 6 residues processed: 132 average time/residue: 2.9141 time to fit residues: 420.8141 Evaluate side-chains 103 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 2.239 ------------------------------------------------------------------------------- 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: 0.8980 chunk 122 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 159 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13701 Z= 0.240 Angle : 0.642 19.907 18463 Z= 0.366 Chirality : 0.040 0.172 2044 Planarity : 0.003 0.075 2341 Dihedral : 7.849 105.348 1926 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.87 % Allowed : 8.10 % Favored : 91.03 % 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: 1.11 (0.21), residues: 1630 helix: 1.37 (0.19), residues: 703 sheet: 0.52 (0.29), residues: 289 loop : 0.27 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 162 HIS 0.004 0.001 HIS B 684 PHE 0.014 0.001 PHE C 120 TYR 0.021 0.002 TYR D 735 ARG 0.005 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 119 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 357 LYS cc_start: 0.7918 (tptt) cc_final: 0.7567 (tttp) REVERT: C 18 GLU cc_start: 0.8632 (tt0) cc_final: 0.8327 (tm-30) outliers start: 13 outliers final: 7 residues processed: 110 average time/residue: 3.1376 time to fit residues: 375.6441 Evaluate side-chains 106 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 2.184 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 110 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 70 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.8792 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13701 Z= 0.176 Angle : 0.599 19.862 18463 Z= 0.338 Chirality : 0.040 0.168 2044 Planarity : 0.003 0.070 2341 Dihedral : 7.064 101.439 1924 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.67 % Allowed : 8.77 % Favored : 90.56 % 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: 1.20 (0.21), residues: 1630 helix: 1.62 (0.20), residues: 704 sheet: 0.47 (0.29), residues: 287 loop : 0.15 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 162 HIS 0.005 0.001 HIS B 684 PHE 0.009 0.001 PHE A 221 TYR 0.016 0.001 TYR D 735 ARG 0.007 0.000 ARG D 633 *********************** 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: 10 poor density : 108 time to evaluate : 2.324 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: 0.7469 (mmm) cc_final: 0.7105 (mmt) REVERT: B 180 MET cc_start: 0.8527 (mtp) cc_final: 0.8208 (mtp) REVERT: B 222 VAL cc_start: 0.9066 (t) cc_final: 0.8847 (m) REVERT: B 357 LYS cc_start: 0.7869 (tptt) cc_final: 0.7493 (tttp) REVERT: C 18 GLU cc_start: 0.8638 (tt0) cc_final: 0.8299 (tm-30) REVERT: C 130 MET cc_start: 0.4961 (mmp) cc_final: 0.4217 (mmm) outliers start: 10 outliers final: 7 residues processed: 113 average time/residue: 3.1783 time to fit residues: 391.3096 Evaluate side-chains 105 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 2.170 ------------------------------------------------------------------------------- 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 C residue 117 MET 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: 5.9990 chunk 88 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 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 : 0.006 0.089 13701 Z= 0.403 Angle : 0.664 19.752 18463 Z= 0.376 Chirality : 0.043 0.217 2044 Planarity : 0.004 0.045 2341 Dihedral : 8.190 109.279 1924 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.20 % Allowed : 8.84 % Favored : 89.96 % 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: 0.87 (0.20), residues: 1630 helix: 1.41 (0.19), residues: 704 sheet: 0.32 (0.29), residues: 293 loop : -0.13 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 557 HIS 0.007 0.002 HIS B 633 PHE 0.014 0.002 PHE D 740 TYR 0.020 0.002 TYR D 735 ARG 0.006 0.001 ARG B 346 *********************** 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 117 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 557 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8483 (mp0) REVERT: B 357 LYS cc_start: 0.7879 (tptt) cc_final: 0.7464 (tttp) outliers start: 18 outliers final: 9 residues processed: 108 average time/residue: 2.9809 time to fit residues: 351.7259 Evaluate side-chains 99 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 2.317 ------------------------------------------------------------------------------- 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 B residue 660 LYS Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 636 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13701 Z= 0.179 Angle : 0.595 19.618 18463 Z= 0.336 Chirality : 0.040 0.171 2044 Planarity : 0.003 0.056 2341 Dihedral : 6.952 86.523 1922 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.80 % Allowed : 9.91 % 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: 1.01 (0.21), residues: 1630 helix: 1.62 (0.20), residues: 704 sheet: 0.31 (0.29), residues: 287 loop : -0.14 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 557 HIS 0.004 0.001 HIS B 633 PHE 0.009 0.001 PHE D 774 TYR 0.016 0.001 TYR D 735 ARG 0.006 0.000 ARG B 201 *********************** 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 109 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 VAL cc_start: 0.9050 (t) cc_final: 0.8825 (m) REVERT: B 357 LYS cc_start: 0.7864 (tptt) cc_final: 0.7470 (tttp) REVERT: C 18 GLU cc_start: 0.8655 (tt0) cc_final: 0.8341 (tm-30) outliers start: 12 outliers final: 8 residues processed: 104 average time/residue: 2.6154 time to fit residues: 300.6587 Evaluate side-chains 100 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 2.174 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 636 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.3793 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= 0.218 Angle : 0.589 19.722 18463 Z= 0.333 Chirality : 0.040 0.166 2044 Planarity : 0.003 0.042 2341 Dihedral : 6.651 85.684 1922 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.80 % Allowed : 10.04 % Favored : 89.16 % 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: 1.10 (0.21), residues: 1630 helix: 1.76 (0.20), residues: 702 sheet: 0.24 (0.29), residues: 293 loop : -0.11 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 557 HIS 0.004 0.001 HIS B 633 PHE 0.007 0.001 PHE D 774 TYR 0.016 0.001 TYR D 735 ARG 0.007 0.000 ARG B 201 *********************** 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 107 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 VAL cc_start: 0.9062 (t) cc_final: 0.8833 (m) REVERT: B 357 LYS cc_start: 0.7889 (tptt) cc_final: 0.7484 (tttp) REVERT: C 18 GLU cc_start: 0.8677 (tt0) cc_final: 0.8351 (tm-30) outliers start: 12 outliers final: 6 residues processed: 101 average time/residue: 2.6688 time to fit residues: 297.5526 Evaluate side-chains 98 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 2.107 ------------------------------------------------------------------------------- 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 123 PHE Chi-restraints excluded: chain D residue 636 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 142 optimal weight: 0.1980 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 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.3893 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= 0.168 Angle : 0.576 19.665 18463 Z= 0.324 Chirality : 0.039 0.159 2044 Planarity : 0.003 0.044 2341 Dihedral : 6.342 83.443 1922 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.60 % Allowed : 10.44 % Favored : 88.96 % 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: 1.20 (0.21), residues: 1630 helix: 1.88 (0.20), residues: 702 sheet: 0.27 (0.29), residues: 287 loop : -0.10 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 557 HIS 0.003 0.001 HIS B 633 PHE 0.007 0.001 PHE D 774 TYR 0.015 0.001 TYR D 735 ARG 0.007 0.000 ARG B 346 *********************** 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 106 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 2.168 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: B 222 VAL cc_start: 0.9057 (t) cc_final: 0.8828 (m) REVERT: B 357 LYS cc_start: 0.7887 (tptt) cc_final: 0.7492 (tttp) REVERT: C 18 GLU cc_start: 0.8657 (tt0) cc_final: 0.8370 (tm-30) outliers start: 9 outliers final: 5 residues processed: 101 average time/residue: 2.6953 time to fit residues: 301.7796 Evaluate side-chains 100 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 2.117 ------------------------------------------------------------------------------- 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 123 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 137 optimal weight: 0.3980 chunk 144 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13701 Z= 0.279 Angle : 0.607 19.652 18463 Z= 0.341 Chirality : 0.040 0.163 2044 Planarity : 0.003 0.047 2341 Dihedral : 6.742 85.300 1922 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.74 % Allowed : 10.24 % Favored : 89.02 % 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: 1.16 (0.21), residues: 1630 helix: 1.92 (0.20), residues: 690 sheet: 0.20 (0.29), residues: 293 loop : -0.14 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 557 HIS 0.005 0.001 HIS B 633 PHE 0.007 0.001 PHE C 103 TYR 0.017 0.002 TYR D 735 ARG 0.008 0.001 ARG B 346 *********************** 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 108 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 VAL cc_start: 0.9045 (t) cc_final: 0.8811 (m) REVERT: C 18 GLU cc_start: 0.8692 (tt0) cc_final: 0.8364 (tm-30) outliers start: 11 outliers final: 4 residues processed: 102 average time/residue: 2.6777 time to fit residues: 302.3177 Evaluate side-chains 97 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 2.119 ------------------------------------------------------------------------------- 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 627 TYR Chi-restraints excluded: chain C residue 123 PHE 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: 0.6980 chunk 106 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.4000 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= 0.200 Angle : 0.596 19.479 18463 Z= 0.332 Chirality : 0.039 0.165 2044 Planarity : 0.003 0.049 2341 Dihedral : 6.449 80.879 1922 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.33 % Allowed : 10.78 % 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: 1.19 (0.21), residues: 1630 helix: 1.97 (0.20), residues: 691 sheet: 0.23 (0.29), residues: 287 loop : -0.17 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 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 0.009 0.000 ARG B 346 ********************** 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 101 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 VAL cc_start: 0.9043 (t) cc_final: 0.8811 (m) REVERT: C 18 GLU cc_start: 0.8665 (tt0) cc_final: 0.8363 (tm-30) outliers start: 5 outliers final: 4 residues processed: 97 average time/residue: 2.7422 time to fit residues: 294.7911 Evaluate side-chains 98 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 2.392 ------------------------------------------------------------------------------- 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 627 TYR Chi-restraints excluded: chain C residue 123 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.079379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.060581 restraints weight = 91506.729| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.61 r_work: 0.2953 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13701 Z= 0.275 Angle : 0.611 19.353 18463 Z= 0.342 Chirality : 0.040 0.167 2044 Planarity : 0.003 0.050 2341 Dihedral : 6.762 82.518 1922 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.47 % Allowed : 10.64 % 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: 1.09 (0.21), residues: 1630 helix: 1.90 (0.20), residues: 691 sheet: 0.17 (0.29), residues: 293 loop : -0.22 (0.24), residues: 646 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 C 103 TYR 0.017 0.002 TYR D 735 ARG 0.009 0.001 ARG B 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8407.04 seconds wall clock time: 146 minutes 9.36 seconds (8769.36 seconds total)