Starting phenix.real_space_refine on Fri Aug 7 09:10:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8poh_17792/08_2026/8poh_17792.cif Found real_map, /net/cci-nas-00/data/ceres_data/8poh_17792/08_2026/8poh_17792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8poh_17792/08_2026/8poh_17792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8poh_17792/08_2026/8poh_17792.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8poh_17792/08_2026/8poh_17792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8poh_17792/08_2026/8poh_17792.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 sd= 0.080 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: 6 Type Number sf(0) Gaussians P 38 5.49 5 Mg 1 5.21 5 S 148 5.16 5 C 12956 2.51 5 N 3589 2.21 5 O 3997 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20729 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4155 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 515, 4143 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 28, 'TRANS': 486} Conformer: "B" Number of residues, atoms: 515, 4143 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 28, 'TRANS': 486} bond proxies already assigned to first conformer: 4218 Chain: "B" Number of atoms: 4954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4954 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 594} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 978 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 8, 'TRANS': 110} Chain breaks: 1 Chain: "R" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 103 Classifications: {'RNA': 5} Modifications used: {'rna2p_pur': 1, 'rna3p_pyr': 4} Link IDs: {'rna3p': 4} Chain: "V" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 310 Classifications: {'RNA': 14} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 10} Chain: "E" Number of atoms: 4155 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 515, 4143 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 28, 'TRANS': 486} Conformer: "B" Number of residues, atoms: 515, 4143 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 28, 'TRANS': 486} bond proxies already assigned to first conformer: 4218 Chain: "F" Number of atoms: 4966 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 623, 4954 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 594} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 623, 4954 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 594} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 5039 Chain: "G" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 694 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 6, 'TRANS': 77} Chain: "S" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 103 Classifications: {'RNA': 5} Modifications used: {'rna2p_pur': 1, 'rna3p_pyr': 4} Link IDs: {'rna3p': 4} Chain: "U" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 310 Classifications: {'RNA': 14} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 10} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ATYR A 464 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 464 " occ=0.50 residue: pdb=" N ATYR E 464 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR E 464 " occ=0.50 residue: pdb=" N ATYR F 557 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR F 557 " occ=0.50 Time building chain proxies: 5.78, per 1000 atoms: 0.28 Number of scatterers: 20729 At special positions: 0 Unit cell: (100.677, 100.677, 200.447, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 148 16.00 P 38 15.00 Mg 1 11.99 O 3997 8.00 N 3589 7.00 C 12956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.49 Conformation dependent library (CDL) restraints added in 1.4 seconds 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4674 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 24 sheets defined 48.6% alpha, 14.4% beta 7 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 302 through 312 removed outlier: 3.813A pdb=" N ASP A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 348 removed outlier: 4.314A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.682A pdb=" N SER A 409 " --> pdb=" O CYS A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 451 Processing helix chain 'A' and resid 453 through 476 removed outlier: 3.984A pdb=" N GLU A 457 " --> pdb=" O CYS A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 538 removed outlier: 4.072A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 579 removed outlier: 3.531A pdb=" N MET A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 604 removed outlier: 3.777A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.557A pdb=" N GLU A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 removed outlier: 4.155A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 715 removed outlier: 3.576A pdb=" N LEU A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 13 through 22 removed outlier: 4.020A pdb=" N ILE B 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 124 Processing helix chain 'B' and resid 138 through 153 removed outlier: 3.551A pdb=" N ASN B 153 " --> pdb=" O VAL B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 176 Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 248 through 265 removed outlier: 4.038A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 removed outlier: 4.284A pdb=" N ASN B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 345 removed outlier: 4.763A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 371 through 374 removed outlier: 4.048A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 371 through 374' Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 428 through 433 removed outlier: 3.570A pdb=" N LYS B 433 " --> pdb=" O LYS B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 472 Processing helix chain 'B' and resid 518 through 536 removed outlier: 4.171A pdb=" N MET B 523 " --> pdb=" O GLU B 519 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER B 524 " --> pdb=" O SER B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.821A pdb=" N LEU B 589 " --> pdb=" O LYS B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 594 removed outlier: 3.657A pdb=" N GLY B 594 " --> pdb=" O VAL B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.590A pdb=" N LEU B 604 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 removed outlier: 3.764A pdb=" N MET B 616 " --> pdb=" O TRP B 613 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 613 through 616' Processing helix chain 'B' and resid 617 through 625 removed outlier: 3.582A pdb=" N CYS B 625 " --> pdb=" O GLN B 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 51 Processing helix chain 'C' and resid 62 through 67 removed outlier: 3.866A pdb=" N MET C 66 " --> pdb=" O ARG C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 102 removed outlier: 3.755A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 115 removed outlier: 4.420A pdb=" N LYS C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 128 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.581A pdb=" N GLN C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 217 removed outlier: 3.623A pdb=" N GLN E 217 " --> pdb=" O ARG E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 235 Processing helix chain 'E' and resid 241 through 249 Processing helix chain 'E' and resid 302 through 312 removed outlier: 3.997A pdb=" N ASP E 306 " --> pdb=" O ILE E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 347 removed outlier: 3.842A pdb=" N TYR E 334 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 370 Processing helix chain 'E' and resid 405 through 415 Processing helix chain 'E' and resid 433 through 451 Processing helix chain 'E' and resid 454 through 476 Processing helix chain 'E' and resid 533 through 538 removed outlier: 3.818A pdb=" N GLU E 538 " --> pdb=" O HIS E 535 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 579 Processing helix chain 'E' and resid 582 through 604 removed outlier: 3.578A pdb=" N LEU E 586 " --> pdb=" O ARG E 582 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN E 590 " --> pdb=" O LEU E 586 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL E 602 " --> pdb=" O ALA E 598 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS E 603 " --> pdb=" O GLU E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 607 through 612 Processing helix chain 'E' and resid 632 through 650 Processing helix chain 'E' and resid 652 through 674 removed outlier: 4.385A pdb=" N LYS E 664 " --> pdb=" O ALA E 660 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU E 665 " --> pdb=" O GLU E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 682 through 692 removed outlier: 3.943A pdb=" N LEU E 686 " --> pdb=" O ASP E 682 " (cutoff:3.500A) Processing helix chain 'E' and resid 697 through 715 removed outlier: 3.630A pdb=" N LEU E 715 " --> pdb=" O LEU E 711 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 11 removed outlier: 3.507A pdb=" N LYS F 11 " --> pdb=" O LEU F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 22 removed outlier: 4.025A pdb=" N ILE F 18 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N SER F 19 " --> pdb=" O ASN F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 49 removed outlier: 3.602A pdb=" N TYR F 49 " --> pdb=" O ARG F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 99 Processing helix chain 'F' and resid 101 through 117 Processing helix chain 'F' and resid 118 through 124 Processing helix chain 'F' and resid 138 through 153 removed outlier: 3.527A pdb=" N ASN F 153 " --> pdb=" O VAL F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 161 removed outlier: 4.226A pdb=" N SER F 160 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 176 removed outlier: 3.646A pdb=" N ASP F 175 " --> pdb=" O MET F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 222 Processing helix chain 'F' and resid 248 through 265 removed outlier: 4.080A pdb=" N LYS F 265 " --> pdb=" O SER F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 292 removed outlier: 4.367A pdb=" N ALA F 280 " --> pdb=" O ASN F 276 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASN F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 326 removed outlier: 3.563A pdb=" N PHE F 318 " --> pdb=" O ASN F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 346 removed outlier: 4.564A pdb=" N ALA F 340 " --> pdb=" O VAL F 336 " (cutoff:3.500A) Proline residue: F 341 - end of helix Processing helix chain 'F' and resid 371 through 375 removed outlier: 4.243A pdb=" N ALA F 374 " --> pdb=" O GLU F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 393 Processing helix chain 'F' and resid 414 through 426 Processing helix chain 'F' and resid 428 through 433 Processing helix chain 'F' and resid 455 through 472 Processing helix chain 'F' and resid 518 through 537 removed outlier: 4.107A pdb=" N MET F 523 " --> pdb=" O GLU F 519 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER F 524 " --> pdb=" O SER F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 560 Processing helix chain 'F' and resid 572 through 583 Processing helix chain 'F' and resid 585 through 589 removed outlier: 3.763A pdb=" N GLY F 588 " --> pdb=" O SER F 585 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU F 589 " --> pdb=" O LYS F 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 585 through 589' Processing helix chain 'F' and resid 590 through 594 Processing helix chain 'F' and resid 607 through 612 Processing helix chain 'F' and resid 613 through 616 removed outlier: 3.619A pdb=" N MET F 616 " --> pdb=" O TRP F 613 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 613 through 616' Processing helix chain 'F' and resid 617 through 625 Processing helix chain 'G' and resid 43 through 51 Processing helix chain 'G' and resid 62 through 67 removed outlier: 3.784A pdb=" N MET G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 102 Processing helix chain 'G' and resid 110 through 115 Processing helix chain 'G' and resid 115 through 125 Processing sheet with id=AA1, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.624A pdb=" N GLY B 304 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 447 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 290 through 292 removed outlier: 6.656A pdb=" N ARG A 496 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N THR A 491 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N THR A 498 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ARG A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 322 through 324 removed outlier: 6.438A pdb=" N ILE A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU A 544 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU A 549 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL A 557 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG A 551 " --> pdb=" O GLY A 555 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLY A 555 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG A 496 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N THR A 491 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N THR A 498 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ARG A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 353 through 355 Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 378 removed outlier: 6.095A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 627 through 631 removed outlier: 6.930A pdb=" N GLY A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLU A 623 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 182 Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 243 removed outlier: 7.019A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB3, first strand: chain 'C' and resid 57 through 59 removed outlier: 4.598A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 129 through 135 removed outlier: 5.792A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR C 245 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET C 243 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 258 through 259 removed outlier: 3.608A pdb=" N GLY F 304 " --> pdb=" O PHE F 447 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 290 through 292 removed outlier: 7.522A pdb=" N TYR E 501 " --> pdb=" O PHE E 525 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL E 557 " --> pdb=" O LEU E 549 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU E 549 " --> pdb=" O VAL E 557 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ARG E 559 " --> pdb=" O ASP E 547 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP E 547 " --> pdb=" O ARG E 559 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N MET E 561 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS E 324 " --> pdb=" O VAL E 542 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLU E 544 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE E 322 " --> pdb=" O GLU E 544 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N GLY E 546 " --> pdb=" O PRO E 320 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N MET E 548 " --> pdb=" O LYS E 318 " (cutoff:3.500A) removed outlier: 11.398A pdb=" N LYS E 318 " --> pdb=" O MET E 548 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 290 through 292 removed outlier: 5.295A pdb=" N THR E 498 " --> pdb=" O ARG E 489 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ARG E 489 " --> pdb=" O THR E 498 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU E 500 " --> pdb=" O SER E 487 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N SER E 487 " --> pdb=" O LEU E 500 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY E 502 " --> pdb=" O MET E 485 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 377 through 378 removed outlier: 6.292A pdb=" N GLU E 377 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLN F 367 " --> pdb=" O GLU E 377 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 628 through 631 removed outlier: 6.357A pdb=" N GLY E 631 " --> pdb=" O PRO E 620 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 54 through 57 Processing sheet with id=AC2, first strand: chain 'F' and resid 128 through 130 Processing sheet with id=AC3, first strand: chain 'F' and resid 179 through 182 Processing sheet with id=AC4, first strand: chain 'F' and resid 239 through 243 removed outlier: 4.757A pdb=" N ARG F 239 " --> pdb=" O LYS F 229 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU F 224 " --> pdb=" O ARG F 350 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 489 through 492 Processing sheet with id=AC6, first strand: chain 'G' and resid 57 through 59 removed outlier: 4.444A pdb=" N MET G 90 " --> pdb=" O SER G 79 " (cutoff:3.500A) 968 hydrogen bonds defined for protein. 2682 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6600 1.34 - 1.46: 3659 1.46 - 1.58: 10667 1.58 - 1.70: 73 1.70 - 1.82: 257 Bond restraints: 21256 Sorted by residual: bond pdb=" N PRO E 625 " pdb=" CD PRO E 625 " ideal model delta sigma weight residual 1.473 1.594 -0.121 1.40e-02 5.10e+03 7.47e+01 bond pdb=" C SER E 624 " pdb=" O SER E 624 " ideal model delta sigma weight residual 1.236 1.290 -0.055 1.01e-02 9.80e+03 2.92e+01 bond pdb=" N ILE F 339 " pdb=" CA ILE F 339 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.14e-02 7.69e+03 8.23e+00 bond pdb=" CG PRO E 625 " pdb=" CD PRO E 625 " ideal model delta sigma weight residual 1.503 1.429 0.074 3.40e-02 8.65e+02 4.73e+00 bond pdb=" C SER E 624 " pdb=" N PRO E 625 " ideal model delta sigma weight residual 1.335 1.364 -0.029 1.36e-02 5.41e+03 4.56e+00 ... (remaining 21251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 28555 2.21 - 4.43: 327 4.43 - 6.64: 14 6.64 - 8.85: 5 8.85 - 11.07: 3 Bond angle restraints: 28904 Sorted by residual: angle pdb=" N PRO E 625 " pdb=" CD PRO E 625 " pdb=" CG PRO E 625 " ideal model delta sigma weight residual 103.20 92.13 11.07 1.50e+00 4.44e-01 5.44e+01 angle pdb=" CA PRO E 625 " pdb=" N PRO E 625 " pdb=" CD PRO E 625 " ideal model delta sigma weight residual 112.00 103.79 8.21 1.40e+00 5.10e-01 3.44e+01 angle pdb=" O4' A V 7 " pdb=" C1' A V 7 " pdb=" N9 A V 7 " ideal model delta sigma weight residual 108.20 111.18 -2.98 8.00e-01 1.56e+00 1.38e+01 angle pdb=" C PRO F 341 " pdb=" N ILE F 342 " pdb=" CA ILE F 342 " ideal model delta sigma weight residual 120.56 125.08 -4.52 1.26e+00 6.30e-01 1.29e+01 angle pdb=" CB MET F 171 " pdb=" CG MET F 171 " pdb=" SD MET F 171 " ideal model delta sigma weight residual 112.70 123.07 -10.37 3.00e+00 1.11e-01 1.20e+01 ... (remaining 28899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10894 17.96 - 35.91: 1459 35.91 - 53.87: 446 53.87 - 71.82: 138 71.82 - 89.78: 41 Dihedral angle restraints: 12978 sinusoidal: 5749 harmonic: 7229 Sorted by residual: dihedral pdb=" CA ASP A 426 " pdb=" CB ASP A 426 " pdb=" CG ASP A 426 " pdb=" OD1 ASP A 426 " ideal model delta sinusoidal sigma weight residual -30.00 -88.02 58.02 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CB GLU F 575 " pdb=" CG GLU F 575 " pdb=" CD GLU F 575 " pdb=" OE1 GLU F 575 " ideal model delta sinusoidal sigma weight residual 0.00 -89.58 89.58 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG B 468 " pdb=" CD ARG B 468 " pdb=" NE ARG B 468 " pdb=" CZ ARG B 468 " ideal model delta sinusoidal sigma weight residual -90.00 -134.12 44.12 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 12975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2223 0.033 - 0.066: 689 0.066 - 0.098: 158 0.098 - 0.131: 99 0.131 - 0.164: 6 Chirality restraints: 3175 Sorted by residual: chirality pdb=" CA ILE F 339 " pdb=" N ILE F 339 " pdb=" C ILE F 339 " pdb=" CB ILE F 339 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CA PRO E 625 " pdb=" N PRO E 625 " pdb=" C PRO E 625 " pdb=" CB PRO E 625 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CB THR F 42 " pdb=" CA THR F 42 " pdb=" OG1 THR F 42 " pdb=" CG2 THR F 42 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 3172 not shown) Planarity restraints: 3584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 624 " -0.055 5.00e-02 4.00e+02 7.79e-02 9.71e+00 pdb=" N PRO E 625 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO E 625 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 625 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 4 " 0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO B 5 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 5 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 5 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " -0.022 2.00e-02 2.50e+03 9.96e-03 2.73e+00 pdb=" N9 A V 4 " 0.023 2.00e-02 2.50e+03 pdb=" C8 A V 4 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A V 4 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A V 4 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A V 4 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A V 4 " 0.003 2.00e-02 2.50e+03 ... (remaining 3581 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 183 2.58 - 3.16: 16670 3.16 - 3.74: 30858 3.74 - 4.32: 42074 4.32 - 4.90: 73294 Nonbonded interactions: 163079 Sorted by model distance: nonbonded pdb=" OE1 GLU A 610 " pdb=" ND2 ASN A 614 " model vdw 2.001 3.120 nonbonded pdb=" N GLU A 397 " pdb=" OE1 GLU A 397 " model vdw 2.022 3.120 nonbonded pdb=" O2' A V 7 " pdb=" OP2 A V 8 " model vdw 2.024 3.040 nonbonded pdb=" OD2 ASP A 431 " pdb=" OG SER A 440 " model vdw 2.024 3.040 nonbonded pdb=" O2' A U 7 " pdb=" OP2 A U 8 " model vdw 2.070 3.040 ... (remaining 163074 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 202 through 463 or resid 465 through 716)) selection = (chain 'E' and (resid 202 through 463 or resid 465 through 716)) } ncs_group { reference = (chain 'B' and (resid 1 through 556 or resid 558 through 670)) selection = (chain 'F' and (resid 1 through 556 or resid 558 through 670)) } ncs_group { reference = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'U' selection = chain 'V' } 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=0.50 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: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 21.030 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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 : 0.003 0.121 21256 Z= 0.153 Angle : 0.572 11.067 28904 Z= 0.319 Chirality : 0.038 0.164 3175 Planarity : 0.004 0.078 3584 Dihedral : 18.791 89.777 8304 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.37 % Allowed : 29.27 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.17), residues: 2466 helix: 1.42 (0.16), residues: 1118 sheet: 0.60 (0.34), residues: 240 loop : -1.52 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 46 TYR 0.018 0.001 TYR F 253 PHE 0.011 0.001 PHE A 520 TRP 0.007 0.001 TRP A 699 HIS 0.002 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (21256) covalent geometry : angle 0.57249 / 0.32 (28904) hydrogen bonds : bond 0.14722 / 9.91 ( 978) hydrogen bonds : angle 5.64218 / 3.99 ( 2720) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 239 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 278 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8063 (tp-100) REVERT: C 111 TYR cc_start: 0.6517 (OUTLIER) cc_final: 0.5629 (m-80) REVERT: E 497 LYS cc_start: 0.7412 (mtpt) cc_final: 0.7087 (mtmt) outliers start: 52 outliers final: 49 residues processed: 287 average time/residue: 0.1534 time to fit residues: 68.8287 Evaluate side-chains 284 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 233 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 111 TYR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 392 GLN Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 513 ASN Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 607 LEU Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 312 ASN Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 520 SER Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 110 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 105 ASN E 696 ASN F 115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.182835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.139412 restraints weight = 70875.116| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.78 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3681 r_free = 0.3681 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3681 r_free = 0.3681 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21256 Z= 0.192 Angle : 0.623 13.260 28904 Z= 0.318 Chirality : 0.043 0.165 3175 Planarity : 0.004 0.059 3584 Dihedral : 11.093 73.048 3347 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.28 % Allowed : 25.99 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.17), residues: 2466 helix: 1.51 (0.16), residues: 1124 sheet: 0.55 (0.33), residues: 242 loop : -1.52 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 46 TYR 0.023 0.002 TYR A 305 PHE 0.018 0.002 PHE A 520 TRP 0.012 0.001 TRP A 317 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 (21256) covalent geometry : angle 0.62283 / 0.32 (28904) hydrogen bonds : bond 0.05872 / 3.92 ( 978) hydrogen bonds : angle 4.54555 / 3.25 ( 2720) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 265 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7814 (tp-100) REVERT: A 349 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7095 (mm-30) REVERT: B 239 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7377 (ttm110) REVERT: B 284 ASN cc_start: 0.8207 (t0) cc_final: 0.7956 (m-40) REVERT: B 614 GLU cc_start: 0.7509 (tp30) cc_final: 0.7301 (tp30) REVERT: E 413 LYS cc_start: 0.8476 (tptt) cc_final: 0.8086 (tppt) REVERT: F 397 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7415 (tt) outliers start: 94 outliers final: 53 residues processed: 330 average time/residue: 0.1544 time to fit residues: 79.6923 Evaluate side-chains 305 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 248 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 374 MET Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 607 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 116 GLN Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 290 MET Chi-restraints excluded: chain F residue 312 ASN Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain G residue 64 MET Chi-restraints excluded: chain G residue 110 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 226 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 225 optimal weight: 0.8980 chunk 129 optimal weight: 8.9990 chunk 175 optimal weight: 4.9990 chunk 53 optimal weight: 0.3980 chunk 159 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.184976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.142099 restraints weight = 59621.342| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 3.58 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21256 Z= 0.123 Angle : 0.533 10.691 28904 Z= 0.274 Chirality : 0.039 0.174 3175 Planarity : 0.004 0.052 3584 Dihedral : 10.707 73.147 3305 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.55 % Allowed : 25.76 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.17), residues: 2466 helix: 1.71 (0.16), residues: 1124 sheet: 0.74 (0.34), residues: 224 loop : -1.51 (0.17), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 126 TYR 0.016 0.001 TYR A 305 PHE 0.013 0.001 PHE B 490 TRP 0.009 0.001 TRP A 317 HIS 0.002 0.000 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (21256) covalent geometry : angle 0.53280 / 0.27 (28904) hydrogen bonds : bond 0.04663 / 3.11 ( 978) hydrogen bonds : angle 4.28327 / 3.05 ( 2720) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 268 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 626 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7146 (pttt) REVERT: B 239 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7413 (ttm110) REVERT: B 284 ASN cc_start: 0.8022 (t0) cc_final: 0.7770 (m-40) REVERT: E 413 LYS cc_start: 0.8418 (tptt) cc_final: 0.8065 (tppt) REVERT: E 492 LYS cc_start: 0.7767 (tppp) cc_final: 0.7434 (tppt) REVERT: F 241 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8525 (pp) outliers start: 78 outliers final: 54 residues processed: 325 average time/residue: 0.1438 time to fit residues: 72.7794 Evaluate side-chains 308 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 251 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 374 MET Chi-restraints excluded: chain E residue 421 SER Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 607 LEU Chi-restraints excluded: chain F residue 116 GLN Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 290 MET Chi-restraints excluded: chain F residue 305 ASP Chi-restraints excluded: chain F residue 312 ASN Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 64 MET Chi-restraints excluded: chain G residue 110 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 102 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 15 optimal weight: 0.0040 chunk 233 optimal weight: 6.9990 chunk 182 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 230 optimal weight: 6.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.181803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.139872 restraints weight = 52127.528| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 3.20 r_work: 0.3238 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21256 Z= 0.205 Angle : 0.582 11.535 28904 Z= 0.298 Chirality : 0.042 0.169 3175 Planarity : 0.004 0.061 3584 Dihedral : 10.659 73.041 3301 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.87 % Allowed : 25.49 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.17), residues: 2466 helix: 1.56 (0.16), residues: 1124 sheet: 0.53 (0.33), residues: 242 loop : -1.55 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 566 TYR 0.016 0.001 TYR E 687 PHE 0.021 0.001 PHE A 520 TRP 0.013 0.001 TRP A 317 HIS 0.006 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.20 (21256) covalent geometry : angle 0.58209 / 0.30 (28904) hydrogen bonds : bond 0.05467 / 3.64 ( 978) hydrogen bonds : angle 4.37658 / 3.13 ( 2720) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 253 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 397 GLU cc_start: 0.7557 (pm20) cc_final: 0.7252 (pm20) REVERT: A 626 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7505 (pttt) REVERT: B 239 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7655 (ttm110) REVERT: B 284 ASN cc_start: 0.8479 (t0) cc_final: 0.8139 (m-40) REVERT: E 413 LYS cc_start: 0.8760 (tptt) cc_final: 0.8334 (tppt) REVERT: E 492 LYS cc_start: 0.8056 (tppp) cc_final: 0.7747 (tppt) REVERT: E 597 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7117 (mm-30) REVERT: F 241 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7855 (pp) REVERT: F 316 ARG cc_start: 0.6289 (mtt180) cc_final: 0.5477 (mtm180) REVERT: G 48 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7503 (mttm) outliers start: 85 outliers final: 63 residues processed: 315 average time/residue: 0.1441 time to fit residues: 70.6744 Evaluate side-chains 317 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 249 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 374 MET Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 597 GLU Chi-restraints excluded: chain E residue 607 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 116 GLN Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 290 MET Chi-restraints excluded: chain F residue 312 ASN Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 523 MET Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 64 MET Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 110 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 112 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 209 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** 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 = 0.4140 r_free = 0.4140 target = 0.185419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.134709 restraints weight = 49844.947| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 4.03 r_work: 0.3248 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21256 Z= 0.183 Angle : 0.569 10.676 28904 Z= 0.293 Chirality : 0.041 0.177 3175 Planarity : 0.004 0.061 3584 Dihedral : 10.647 73.029 3300 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.60 % Allowed : 25.03 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.17), residues: 2466 helix: 1.53 (0.16), residues: 1120 sheet: 0.49 (0.33), residues: 242 loop : -1.60 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 572 TYR 0.015 0.001 TYR E 687 PHE 0.018 0.001 PHE A 520 TRP 0.012 0.001 TRP A 317 HIS 0.005 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.18 (21256) covalent geometry : angle 0.56926 / 0.29 (28904) hydrogen bonds : bond 0.05327 / 3.55 ( 978) hydrogen bonds : angle 4.34855 / 3.10 ( 2720) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 258 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 248 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7778 (mt0) REVERT: A 626 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7429 (pttt) REVERT: B 239 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7799 (ttm110) REVERT: B 284 ASN cc_start: 0.8444 (t0) cc_final: 0.7958 (m-40) REVERT: E 394 ASP cc_start: 0.7457 (t70) cc_final: 0.7222 (t0) REVERT: E 413 LYS cc_start: 0.8719 (tptt) cc_final: 0.8289 (tppt) REVERT: E 597 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6894 (mm-30) REVERT: F 111 MET cc_start: 0.7649 (mtm) cc_final: 0.6956 (tpp) REVERT: F 235 LYS cc_start: 0.7928 (mtpt) cc_final: 0.7491 (mtmt) REVERT: F 241 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7647 (pp) REVERT: G 48 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7288 (mttm) outliers start: 101 outliers final: 73 residues processed: 335 average time/residue: 0.1369 time to fit residues: 71.4637 Evaluate side-chains 327 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 248 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 374 MET Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 421 SER Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 597 GLU Chi-restraints excluded: chain E residue 607 LEU Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 116 GLN Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 290 MET Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain F residue 624 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 64 MET Chi-restraints excluded: chain G residue 87 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 245 optimal weight: 10.0000 chunk 227 optimal weight: 2.9990 chunk 88 optimal weight: 0.1980 chunk 86 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 232 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 211 optimal weight: 10.0000 chunk 226 optimal weight: 0.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.181643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.140885 restraints weight = 45054.393| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 5.26 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3702 r_free = 0.3702 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3702 r_free = 0.3702 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21256 Z= 0.174 Angle : 0.565 12.845 28904 Z= 0.289 Chirality : 0.040 0.172 3175 Planarity : 0.004 0.066 3584 Dihedral : 10.544 72.963 3293 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.28 % Allowed : 25.08 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.17), residues: 2466 helix: 1.52 (0.16), residues: 1122 sheet: 0.50 (0.33), residues: 242 loop : -1.62 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 212 TYR 0.014 0.001 TYR A 540 PHE 0.019 0.001 PHE F 381 TRP 0.012 0.001 TRP A 317 HIS 0.005 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.17 (21256) covalent geometry : angle 0.56462 / 0.29 (28904) hydrogen bonds : bond 0.05179 / 3.46 ( 978) hydrogen bonds : angle 4.31746 / 3.07 ( 2720) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 258 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 626 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7257 (pttt) REVERT: B 239 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7510 (ttm110) REVERT: E 413 LYS cc_start: 0.8495 (tptt) cc_final: 0.8159 (tppt) REVERT: E 597 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7082 (mm-30) REVERT: F 241 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8488 (pp) REVERT: G 48 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7556 (mttm) outliers start: 94 outliers final: 73 residues processed: 327 average time/residue: 0.1331 time to fit residues: 67.9818 Evaluate side-chains 324 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 246 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 374 MET Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain E residue 597 GLU Chi-restraints excluded: chain E residue 607 LEU Chi-restraints excluded: chain E residue 666 LEU Chi-restraints excluded: chain E residue 697 ASP Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 116 GLN Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 290 MET Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 523 MET Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain F residue 624 LEU Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 64 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 236 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 139 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 ASN B 425 ASN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 HIS G 110 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.183295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.137919 restraints weight = 49569.100| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.29 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21256 Z= 0.131 Angle : 0.537 12.437 28904 Z= 0.274 Chirality : 0.039 0.180 3175 Planarity : 0.004 0.061 3584 Dihedral : 10.445 72.953 3292 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.91 % Allowed : 25.94 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.17), residues: 2466 helix: 1.68 (0.16), residues: 1122 sheet: 0.54 (0.33), residues: 242 loop : -1.55 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 260 TYR 0.012 0.001 TYR E 687 PHE 0.017 0.001 PHE F 381 TRP 0.011 0.001 TRP B 437 HIS 0.004 0.001 HIS G 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (21256) covalent geometry : angle 0.53675 / 0.27 (28904) hydrogen bonds : bond 0.04478 / 2.99 ( 978) hydrogen bonds : angle 4.18398 / 2.98 ( 2720) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 257 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7580 (mt0) REVERT: A 349 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7144 (mm-30) REVERT: A 626 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7269 (pttt) REVERT: B 239 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7376 (ttm110) REVERT: E 413 LYS cc_start: 0.8436 (tptt) cc_final: 0.8100 (tppt) REVERT: F 241 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8639 (pp) REVERT: F 316 ARG cc_start: 0.5451 (mtt180) cc_final: 0.5183 (mtm180) REVERT: G 48 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7593 (mttm) REVERT: G 61 LYS cc_start: 0.8206 (mptt) cc_final: 0.7990 (mtmm) outliers start: 86 outliers final: 68 residues processed: 319 average time/residue: 0.1446 time to fit residues: 71.9576 Evaluate side-chains 322 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 248 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 374 MET Chi-restraints excluded: chain E residue 421 SER Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 607 LEU Chi-restraints excluded: chain E residue 666 LEU Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 116 GLN Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 290 MET Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 64 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 194 optimal weight: 6.9990 chunk 243 optimal weight: 0.9990 chunk 88 optimal weight: 0.4980 chunk 188 optimal weight: 10.0000 chunk 176 optimal weight: 0.5980 chunk 149 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 7 optimal weight: 0.0570 chunk 166 optimal weight: 7.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 GLN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.187329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.146153 restraints weight = 48893.046| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 5.35 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21256 Z= 0.125 Angle : 0.534 13.881 28904 Z= 0.271 Chirality : 0.039 0.182 3175 Planarity : 0.004 0.057 3584 Dihedral : 10.401 72.925 3292 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.64 % Allowed : 26.08 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.17), residues: 2466 helix: 1.76 (0.16), residues: 1120 sheet: 0.59 (0.32), residues: 242 loop : -1.54 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 260 TYR 0.012 0.001 TYR E 687 PHE 0.018 0.001 PHE F 381 TRP 0.010 0.001 TRP A 317 HIS 0.003 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (21256) covalent geometry : angle 0.53359 / 0.27 (28904) hydrogen bonds : bond 0.04299 / 2.87 ( 978) hydrogen bonds : angle 4.12551 / 2.94 ( 2720) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 256 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7645 (mt0) REVERT: A 349 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7300 (mm-30) REVERT: A 626 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7264 (pttt) REVERT: B 239 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7375 (ttm110) REVERT: C 90 MET cc_start: 0.7796 (mmp) cc_final: 0.7552 (mmm) REVERT: E 413 LYS cc_start: 0.8421 (tptt) cc_final: 0.8126 (tppt) REVERT: F 241 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8611 (pp) REVERT: G 61 LYS cc_start: 0.8103 (mptt) cc_final: 0.7815 (mtmm) outliers start: 80 outliers final: 63 residues processed: 313 average time/residue: 0.1419 time to fit residues: 69.6217 Evaluate side-chains 319 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 251 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 374 MET Chi-restraints excluded: chain E residue 421 SER Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 607 LEU Chi-restraints excluded: chain E residue 666 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 116 GLN Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 290 MET Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 523 MET Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain F residue 624 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 64 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 191 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 189 optimal weight: 20.0000 chunk 137 optimal weight: 0.2980 chunk 201 optimal weight: 10.0000 chunk 53 optimal weight: 0.3980 chunk 29 optimal weight: 5.9990 chunk 141 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 ASN F 306 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.185280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.142727 restraints weight = 55822.503| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 3.38 r_work: 0.3281 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 21256 Z= 0.104 Angle : 0.519 14.642 28904 Z= 0.262 Chirality : 0.038 0.177 3175 Planarity : 0.004 0.055 3584 Dihedral : 10.321 72.916 3290 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.23 % Allowed : 26.17 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.17), residues: 2466 helix: 1.87 (0.16), residues: 1122 sheet: 0.66 (0.32), residues: 242 loop : -1.55 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 496 TYR 0.011 0.001 TYR E 687 PHE 0.018 0.001 PHE F 381 TRP 0.010 0.001 TRP A 699 HIS 0.006 0.001 HIS G 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (21256) covalent geometry : angle 0.51921 / 0.26 (28904) hydrogen bonds : bond 0.03774 / 2.52 ( 978) hydrogen bonds : angle 4.04027 / 2.87 ( 2720) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 260 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7819 (mt0) REVERT: A 349 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7097 (mm-30) REVERT: A 626 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7499 (pttt) REVERT: B 239 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7530 (ttm110) REVERT: B 411 MET cc_start: 0.8767 (mtp) cc_final: 0.8392 (mtm) REVERT: E 413 LYS cc_start: 0.8782 (tptt) cc_final: 0.8430 (tppt) REVERT: E 597 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7081 (mm-30) outliers start: 71 outliers final: 52 residues processed: 312 average time/residue: 0.1449 time to fit residues: 70.1871 Evaluate side-chains 312 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 255 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 374 MET Chi-restraints excluded: chain E residue 421 SER Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 597 GLU Chi-restraints excluded: chain E residue 607 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 116 GLN Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 290 MET Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain G residue 45 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 155 optimal weight: 0.2980 chunk 104 optimal weight: 2.9990 chunk 228 optimal weight: 0.8980 chunk 208 optimal weight: 0.8980 chunk 207 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 183 optimal weight: 0.0870 chunk 80 optimal weight: 2.9990 chunk 242 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 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 = 0.4172 r_free = 0.4172 target = 0.188554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.145518 restraints weight = 44220.644| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 5.32 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21256 Z= 0.115 Angle : 0.534 16.068 28904 Z= 0.269 Chirality : 0.039 0.317 3175 Planarity : 0.004 0.056 3584 Dihedral : 10.296 72.902 3287 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.96 % Allowed : 26.63 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.17), residues: 2466 helix: 1.86 (0.16), residues: 1122 sheet: 0.49 (0.32), residues: 252 loop : -1.53 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 496 TYR 0.019 0.001 TYR F 253 PHE 0.018 0.001 PHE F 381 TRP 0.009 0.001 TRP A 317 HIS 0.002 0.000 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (21256) covalent geometry : angle 0.53437 / 0.27 (28904) hydrogen bonds : bond 0.03939 / 2.63 ( 978) hydrogen bonds : angle 4.05355 / 2.88 ( 2720) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 259 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7654 (mt0) REVERT: A 349 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7354 (mm-30) REVERT: B 239 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7397 (ttm110) REVERT: B 411 MET cc_start: 0.8373 (mtp) cc_final: 0.7968 (mtm) REVERT: E 293 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7128 (mt-10) REVERT: E 413 LYS cc_start: 0.8414 (tptt) cc_final: 0.8077 (tppt) REVERT: E 597 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7070 (mm-30) outliers start: 65 outliers final: 57 residues processed: 307 average time/residue: 0.1439 time to fit residues: 69.2085 Evaluate side-chains 315 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 253 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 374 MET Chi-restraints excluded: chain E residue 421 SER Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 597 GLU Chi-restraints excluded: chain E residue 607 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 116 GLN Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain F residue 290 MET Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain G residue 45 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 131 optimal weight: 0.3980 chunk 177 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 200 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 189 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 591 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.180277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.136291 restraints weight = 49417.946| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 3.34 r_work: 0.3212 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21256 Z= 0.222 Angle : 0.625 16.410 28904 Z= 0.317 Chirality : 0.043 0.202 3175 Planarity : 0.005 0.060 3584 Dihedral : 10.463 72.879 3287 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.10 % Allowed : 26.67 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.17), residues: 2466 helix: 1.50 (0.16), residues: 1126 sheet: 0.33 (0.32), residues: 252 loop : -1.60 (0.17), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 496 TYR 0.017 0.002 TYR A 540 PHE 0.023 0.002 PHE A 520 TRP 0.014 0.001 TRP A 317 HIS 0.006 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.22 (21256) covalent geometry : angle 0.62532 / 0.32 (28904) hydrogen bonds : bond 0.05627 / 3.74 ( 978) hydrogen bonds : angle 4.34261 / 3.10 ( 2720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4014.25 seconds wall clock time: 69 minutes 53.82 seconds (4193.82 seconds total)