Starting phenix.real_space_refine on Wed Jun 18 03:38:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8poh_17792/06_2025/8poh_17792.cif Found real_map, /net/cci-nas-00/data/ceres_data/8poh_17792/06_2025/8poh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8poh_17792/06_2025/8poh_17792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8poh_17792/06_2025/8poh_17792.map" model { file = "/net/cci-nas-00/data/ceres_data/8poh_17792/06_2025/8poh_17792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8poh_17792/06_2025/8poh_17792.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 19.42, per 1000 atoms: 0.94 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: 5.36 Conformation dependent library (CDL) restraints added in 4.1 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: 7.46 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: 7.83 Time building geometry restraints manager: 6.40 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: 28575 2.21 - 4.43: 307 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=" 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 angle pdb=" C SER F 338 " pdb=" N ILE F 339 " pdb=" CA ILE F 339 " ideal model delta sigma weight residual 120.60 124.87 -4.27 1.29e+00 6.01e-01 1.09e+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: 2244 0.033 - 0.066: 708 0.066 - 0.098: 141 0.098 - 0.131: 76 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: 3.560 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: 0.030 Extract box with map and model: 0.940 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 63.250 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.140 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:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 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= 0.149 Angle : 0.559 11.067 28904 Z= 0.294 Chirality : 0.036 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (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 TRP 0.007 0.001 TRP A 699 HIS 0.002 0.001 HIS B 99 PHE 0.011 0.001 PHE A 520 TYR 0.018 0.001 TYR F 253 ARG 0.004 0.000 ARG C 46 Details of bonding type rmsd hydrogen bonds : bond 0.14722 ( 978) hydrogen bonds : angle 5.64218 ( 2720) covalent geometry : bond 0.00308 (21256) covalent geometry : angle 0.55926 (28904) *********************** 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 : 2.270 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: 0.3405 time to fit residues: 151.6611 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 : 2.324 ------------------------------------------------------------------------------- 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 208 optimal weight: 6.9990 chunk 187 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 chunk 193 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 chunk 224 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN B 105 ASN C 233 HIS ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 696 ASN F 115 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.177803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.137860 restraints weight = 46202.575| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 5.15 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 21256 Z= 0.349 Angle : 0.744 14.111 28904 Z= 0.380 Chirality : 0.048 0.199 3175 Planarity : 0.005 0.070 3584 Dihedral : 11.297 73.065 3347 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 5.23 % Allowed : 25.76 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.17), residues: 2466 helix: 1.10 (0.16), residues: 1123 sheet: 0.27 (0.32), residues: 244 loop : -1.66 (0.17), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 317 HIS 0.007 0.001 HIS B 605 PHE 0.029 0.002 PHE A 520 TYR 0.036 0.003 TYR A 305 ARG 0.007 0.001 ARG B 572 Details of bonding type rmsd hydrogen bonds : bond 0.07363 ( 978) hydrogen bonds : angle 4.85106 ( 2720) covalent geometry : bond 0.00863 (21256) covalent geometry : angle 0.74398 (28904) *********************** 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 370 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 255 time to evaluate : 4.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.7997 (tp-100) REVERT: A 626 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7284 (pttt) REVERT: C 243 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.5528 (mpt) REVERT: E 413 LYS cc_start: 0.8493 (tptt) cc_final: 0.8181 (tppt) outliers start: 115 outliers final: 65 residues processed: 330 average time/residue: 0.4271 time to fit residues: 219.8097 Evaluate side-chains 304 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 236 time to evaluate : 2.638 ------------------------------------------------------------------------------- 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 278 GLN 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 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 173 SER 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 285 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 389 ILE 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 543 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 243 MET 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 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 607 LEU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 116 GLN 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 303 THR 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 F residue 523 MET 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 62 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 185 optimal weight: 8.9990 chunk 136 optimal weight: 0.8980 chunk 231 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 241 optimal weight: 0.0570 chunk 213 optimal weight: 10.0000 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.184354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.142730 restraints weight = 39225.293| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 4.76 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 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 = 0.3727 r_free = 0.3727 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1327 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= 0.117 Angle : 0.533 10.095 28904 Z= 0.272 Chirality : 0.039 0.217 3175 Planarity : 0.004 0.054 3584 Dihedral : 10.686 73.088 3310 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.37 % Allowed : 26.58 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.17), residues: 2466 helix: 1.64 (0.16), residues: 1122 sheet: 0.58 (0.33), residues: 224 loop : -1.56 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 437 HIS 0.002 0.000 HIS B 605 PHE 0.015 0.001 PHE B 490 TYR 0.012 0.001 TYR E 687 ARG 0.004 0.000 ARG C 46 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 978) hydrogen bonds : angle 4.23541 ( 2720) covalent geometry : bond 0.00267 (21256) covalent geometry : angle 0.53307 (28904) *********************** 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 340 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 266 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 TYR cc_start: 0.7906 (m-80) cc_final: 0.7700 (m-80) REVERT: A 626 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7253 (pttt) REVERT: B 239 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7156 (ttm110) REVERT: E 413 LYS cc_start: 0.8370 (tptt) cc_final: 0.8046 (tppt) REVERT: E 492 LYS cc_start: 0.7767 (tppp) cc_final: 0.7495 (tppt) REVERT: F 241 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8464 (pp) outliers start: 74 outliers final: 45 residues processed: 315 average time/residue: 0.3443 time to fit residues: 165.5486 Evaluate side-chains 293 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 245 time to evaluate : 2.250 ------------------------------------------------------------------------------- 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 419 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 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 172 ASP 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 391 LYS Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 552 ILE 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 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 473 SER 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 108 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 434 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain G residue 47 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 65 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 241 optimal weight: 0.7980 chunk 189 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.184238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.143942 restraints weight = 41378.575| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 4.56 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1534 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= 0.119 Angle : 0.529 13.243 28904 Z= 0.265 Chirality : 0.039 0.191 3175 Planarity : 0.004 0.054 3584 Dihedral : 10.364 73.055 3292 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.60 % Allowed : 25.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.17), residues: 2466 helix: 1.79 (0.16), residues: 1120 sheet: 0.66 (0.33), residues: 224 loop : -1.57 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 317 HIS 0.003 0.000 HIS B 605 PHE 0.013 0.001 PHE B 490 TYR 0.016 0.001 TYR E 687 ARG 0.003 0.000 ARG C 46 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 978) hydrogen bonds : angle 4.12410 ( 2720) covalent geometry : bond 0.00275 (21256) covalent geometry : angle 0.52921 (28904) *********************** 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 335 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 256 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 239 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7372 (ttm110) REVERT: E 293 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6657 (mt-10) REVERT: E 413 LYS cc_start: 0.8420 (tptt) cc_final: 0.8121 (tppt) REVERT: E 492 LYS cc_start: 0.7758 (tppp) cc_final: 0.7509 (tppt) REVERT: E 497 LYS cc_start: 0.7870 (mtpt) cc_final: 0.7552 (mtpp) REVERT: E 597 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6994 (mm-30) REVERT: F 241 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8601 (pp) REVERT: G 61 LYS cc_start: 0.8049 (mptt) cc_final: 0.7842 (mtmm) outliers start: 79 outliers final: 53 residues processed: 316 average time/residue: 0.3397 time to fit residues: 164.3474 Evaluate side-chains 297 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 240 time to evaluate : 2.276 ------------------------------------------------------------------------------- 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 419 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 571 SER 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 212 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 236 LEU 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 395 LEU 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 552 ILE Chi-restraints excluded: chain B residue 592 SER 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 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 421 SER Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 473 SER 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 86 ASP 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 434 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 624 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 64 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 42 optimal weight: 3.9990 chunk 211 optimal weight: 0.0170 chunk 182 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 9 optimal weight: 0.5980 overall best weight: 1.4622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.182772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137660 restraints weight = 54467.148| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.51 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21256 Z= 0.151 Angle : 0.551 13.367 28904 Z= 0.278 Chirality : 0.040 0.172 3175 Planarity : 0.004 0.057 3584 Dihedral : 10.409 73.025 3291 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.50 % Allowed : 25.76 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.17), residues: 2466 helix: 1.66 (0.16), residues: 1123 sheet: 0.51 (0.32), residues: 242 loop : -1.53 (0.17), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 317 HIS 0.004 0.001 HIS B 605 PHE 0.016 0.001 PHE A 520 TYR 0.014 0.001 TYR E 687 ARG 0.003 0.000 ARG B 572 Details of bonding type rmsd hydrogen bonds : bond 0.04773 ( 978) hydrogen bonds : angle 4.18838 ( 2720) covalent geometry : bond 0.00361 (21256) covalent geometry : angle 0.55101 (28904) *********************** 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 334 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 257 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7273 (pttt) REVERT: B 239 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7396 (ttm110) REVERT: E 293 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6769 (mt-10) REVERT: E 413 LYS cc_start: 0.8523 (tptt) cc_final: 0.8152 (tppt) REVERT: E 492 LYS cc_start: 0.7678 (tppp) cc_final: 0.7436 (tppt) REVERT: E 497 LYS cc_start: 0.7865 (mtpt) cc_final: 0.7512 (mtpp) REVERT: E 597 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6905 (mm-30) outliers start: 77 outliers final: 57 residues processed: 310 average time/residue: 0.3308 time to fit residues: 158.1078 Evaluate side-chains 305 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 244 time to evaluate : 2.434 ------------------------------------------------------------------------------- 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 419 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 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 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 391 LYS Chi-restraints excluded: chain B residue 395 LEU 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 552 ILE Chi-restraints excluded: chain B residue 592 SER 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 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 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 E residue 644 SER 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 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 624 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 64 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 192 optimal weight: 6.9990 chunk 85 optimal weight: 0.1980 chunk 166 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 153 optimal weight: 0.5980 chunk 217 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 158 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 ASN ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.185973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.143872 restraints weight = 54573.223| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 3.31 r_work: 0.3288 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 21256 Z= 0.099 Angle : 0.505 14.812 28904 Z= 0.254 Chirality : 0.038 0.169 3175 Planarity : 0.004 0.052 3584 Dihedral : 10.282 72.999 3289 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.91 % Allowed : 26.08 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.17), residues: 2466 helix: 1.91 (0.16), residues: 1122 sheet: 0.67 (0.33), residues: 232 loop : -1.51 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 437 HIS 0.002 0.000 HIS E 326 PHE 0.012 0.001 PHE B 490 TYR 0.012 0.001 TYR E 687 ARG 0.005 0.000 ARG A 496 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 978) hydrogen bonds : angle 3.99455 ( 2720) covalent geometry : bond 0.00225 (21256) covalent geometry : angle 0.50467 (28904) *********************** 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 335 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 271 time to evaluate : 2.441 Fit side-chains revert: symmetry clash REVERT: B 239 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7501 (ttm110) REVERT: B 411 MET cc_start: 0.8692 (mtp) cc_final: 0.8316 (mtm) REVERT: B 614 GLU cc_start: 0.8671 (tp30) cc_final: 0.8394 (tp30) REVERT: C 55 TYR cc_start: 0.8376 (m-80) cc_final: 0.8045 (m-80) REVERT: E 293 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7285 (mt-10) REVERT: E 394 ASP cc_start: 0.7443 (t70) cc_final: 0.7134 (t0) REVERT: E 413 LYS cc_start: 0.8809 (tptt) cc_final: 0.8420 (tppt) REVERT: E 497 LYS cc_start: 0.7904 (mtpt) cc_final: 0.7494 (mtpp) REVERT: E 597 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.7017 (mm-30) REVERT: F 116 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.6429 (mp10) REVERT: F 316 ARG cc_start: 0.6200 (mtt180) cc_final: 0.5846 (mtm180) REVERT: F 344 PHE cc_start: 0.7989 (m-80) cc_final: 0.7568 (m-80) outliers start: 64 outliers final: 47 residues processed: 314 average time/residue: 0.3310 time to fit residues: 160.3778 Evaluate side-chains 301 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 250 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 419 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 506 LYS 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 212 LEU 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 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 533 ASN Chi-restraints excluded: chain B residue 543 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 89 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 450 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 644 SER 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 434 THR Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 624 LEU Chi-restraints excluded: chain G residue 47 MET 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 143 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 197 optimal weight: 0.0000 chunk 37 optimal weight: 0.9990 chunk 66 optimal weight: 0.0370 chunk 72 optimal weight: 0.0470 chunk 194 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 overall best weight: 0.3960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN A 591 GLN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.187457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.144118 restraints weight = 59754.984| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 3.57 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 21256 Z= 0.095 Angle : 0.498 10.691 28904 Z= 0.250 Chirality : 0.038 0.274 3175 Planarity : 0.004 0.050 3584 Dihedral : 10.211 72.976 3285 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.00 % Allowed : 25.76 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.17), residues: 2466 helix: 1.96 (0.16), residues: 1126 sheet: 0.72 (0.33), residues: 232 loop : -1.46 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 699 HIS 0.002 0.000 HIS E 326 PHE 0.014 0.001 PHE F 254 TYR 0.022 0.001 TYR F 253 ARG 0.006 0.000 ARG A 496 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 978) hydrogen bonds : angle 3.93320 ( 2720) covalent geometry : bond 0.00215 (21256) covalent geometry : angle 0.49829 (28904) *********************** 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 335 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 269 time to evaluate : 2.502 Fit side-chains REVERT: A 349 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7142 (mm-30) REVERT: A 626 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7196 (pttt) REVERT: B 239 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7407 (ttm110) REVERT: B 411 MET cc_start: 0.8238 (mtp) cc_final: 0.7849 (mtm) REVERT: B 614 GLU cc_start: 0.7895 (tp30) cc_final: 0.7678 (tp30) REVERT: C 55 TYR cc_start: 0.8278 (m-80) cc_final: 0.8036 (m-80) REVERT: E 293 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6862 (mt-10) REVERT: E 413 LYS cc_start: 0.8454 (tptt) cc_final: 0.8089 (tppt) REVERT: E 497 LYS cc_start: 0.7721 (mtpt) cc_final: 0.7463 (mtpp) REVERT: F 116 GLN cc_start: 0.6466 (OUTLIER) cc_final: 0.5797 (mp10) REVERT: F 224 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7604 (pp) REVERT: F 344 PHE cc_start: 0.7262 (m-80) cc_final: 0.6982 (m-80) outliers start: 66 outliers final: 47 residues processed: 314 average time/residue: 0.3488 time to fit residues: 167.6938 Evaluate side-chains 309 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 256 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ASN 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 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 506 LYS 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 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 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 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 73 GLN Chi-restraints excluded: chain C residue 89 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 450 VAL Chi-restraints excluded: chain E residue 548 MET 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 224 LEU Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 47 MET 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 14 optimal weight: 4.9990 chunk 226 optimal weight: 4.9990 chunk 214 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 125 optimal weight: 40.0000 chunk 32 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 191 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 591 GLN A 713 HIS ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 ASN ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.179295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.135650 restraints weight = 58914.150| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.67 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 21256 Z= 0.259 Angle : 0.637 13.672 28904 Z= 0.323 Chirality : 0.043 0.171 3175 Planarity : 0.005 0.057 3584 Dihedral : 10.458 72.949 3285 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.46 % Allowed : 25.26 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2466 helix: 1.43 (0.16), residues: 1127 sheet: 0.46 (0.32), residues: 244 loop : -1.59 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 317 HIS 0.005 0.001 HIS A 510 PHE 0.025 0.002 PHE A 520 TYR 0.017 0.002 TYR A 540 ARG 0.018 0.001 ARG F 316 Details of bonding type rmsd hydrogen bonds : bond 0.06080 ( 978) hydrogen bonds : angle 4.42268 ( 2720) covalent geometry : bond 0.00642 (21256) covalent geometry : angle 0.63683 (28904) *********************** 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 327 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 251 time to evaluate : 2.252 Fit side-chains revert: symmetry clash REVERT: A 349 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7167 (mm-30) REVERT: A 626 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7331 (pttt) REVERT: B 248 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.8025 (mt) REVERT: B 344 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.9139 (m-80) REVERT: E 293 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6858 (mt-10) REVERT: E 413 LYS cc_start: 0.8474 (tptt) cc_final: 0.8093 (tppt) REVERT: E 497 LYS cc_start: 0.7928 (mtpt) cc_final: 0.7582 (mtpp) REVERT: E 597 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6967 (mm-30) REVERT: F 116 GLN cc_start: 0.6597 (OUTLIER) cc_final: 0.5921 (mp10) REVERT: F 174 MET cc_start: 0.6156 (tmm) cc_final: 0.5890 (pmm) REVERT: F 224 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8039 (pp) REVERT: F 344 PHE cc_start: 0.7453 (m-80) cc_final: 0.7161 (m-80) outliers start: 76 outliers final: 58 residues processed: 310 average time/residue: 0.3339 time to fit residues: 158.4455 Evaluate side-chains 311 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 245 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ASN 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 358 LYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 364 SER 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 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 92 MET 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 248 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 361 SER 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 533 ASN Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 552 ILE 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 117 THR 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 382 GLU 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 504 ILE 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 644 SER 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 224 LEU Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 47 MET 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 230 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 125 optimal weight: 40.0000 chunk 70 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 206 optimal weight: 8.9990 chunk 143 optimal weight: 9.9990 chunk 176 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.183885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.140209 restraints weight = 65611.074| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 3.73 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21256 Z= 0.115 Angle : 0.533 13.885 28904 Z= 0.268 Chirality : 0.038 0.181 3175 Planarity : 0.004 0.053 3584 Dihedral : 10.322 72.972 3285 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.69 % Allowed : 25.90 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2466 helix: 1.71 (0.16), residues: 1126 sheet: 0.59 (0.33), residues: 232 loop : -1.55 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 437 HIS 0.003 0.000 HIS B 605 PHE 0.013 0.001 PHE B 490 TYR 0.020 0.001 TYR F 253 ARG 0.007 0.000 ARG A 496 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 978) hydrogen bonds : angle 4.11282 ( 2720) covalent geometry : bond 0.00268 (21256) covalent geometry : angle 0.53263 (28904) *********************** 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 319 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 260 time to evaluate : 3.190 Fit side-chains revert: symmetry clash REVERT: A 248 GLN cc_start: 0.7801 (mt0) cc_final: 0.7572 (mp10) REVERT: A 349 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7154 (mm-30) REVERT: A 626 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7287 (pttt) REVERT: B 239 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7514 (ttm110) REVERT: B 411 MET cc_start: 0.8337 (mtp) cc_final: 0.7916 (mtm) REVERT: C 55 TYR cc_start: 0.8278 (m-80) cc_final: 0.8055 (m-80) REVERT: E 293 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6853 (mt-10) REVERT: E 413 LYS cc_start: 0.8418 (tptt) cc_final: 0.8049 (tppt) REVERT: E 497 LYS cc_start: 0.7831 (mtpt) cc_final: 0.7542 (mtpp) REVERT: F 116 GLN cc_start: 0.6533 (OUTLIER) cc_final: 0.5786 (mp10) REVERT: F 224 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7909 (pp) REVERT: F 344 PHE cc_start: 0.7379 (m-80) cc_final: 0.7098 (m-80) outliers start: 59 outliers final: 48 residues processed: 304 average time/residue: 0.3303 time to fit residues: 155.9451 Evaluate side-chains 305 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 251 time to evaluate : 2.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ASN 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 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 473 SER Chi-restraints excluded: chain A residue 506 LYS 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 92 MET 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 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 533 ASN Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 552 ILE 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 73 GLN 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 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 450 VAL Chi-restraints excluded: chain E residue 607 LEU Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 116 GLN Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 47 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 192 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 228 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 176 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4128 r_free = 0.4128 target = 0.184194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139380 restraints weight = 53026.785| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.51 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21256 Z= 0.115 Angle : 0.525 12.761 28904 Z= 0.264 Chirality : 0.038 0.174 3175 Planarity : 0.004 0.054 3584 Dihedral : 10.263 72.966 3285 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.37 % Allowed : 26.17 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.17), residues: 2466 helix: 1.78 (0.16), residues: 1127 sheet: 0.61 (0.33), residues: 232 loop : -1.52 (0.17), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 317 HIS 0.002 0.000 HIS B 605 PHE 0.013 0.001 PHE E 381 TYR 0.019 0.001 TYR F 253 ARG 0.006 0.000 ARG A 496 Details of bonding type rmsd hydrogen bonds : bond 0.03966 ( 978) hydrogen bonds : angle 4.06147 ( 2720) covalent geometry : bond 0.00269 (21256) covalent geometry : angle 0.52524 (28904) ********************** 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 309 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 257 time to evaluate : 2.537 Fit side-chains revert: symmetry clash REVERT: A 248 GLN cc_start: 0.7744 (mt0) cc_final: 0.7535 (mp10) REVERT: A 349 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7228 (mm-30) REVERT: A 626 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7581 (pttp) REVERT: B 239 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7836 (ttm110) REVERT: B 411 MET cc_start: 0.8347 (mtp) cc_final: 0.7920 (mtm) REVERT: C 55 TYR cc_start: 0.8225 (m-80) cc_final: 0.7998 (m-80) REVERT: E 293 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6961 (mt-10) REVERT: E 413 LYS cc_start: 0.8438 (tptt) cc_final: 0.8078 (tppt) REVERT: E 497 LYS cc_start: 0.7786 (mtpt) cc_final: 0.7515 (mtpp) REVERT: F 20 THR cc_start: 0.8357 (m) cc_final: 0.8149 (m) REVERT: F 116 GLN cc_start: 0.6604 (OUTLIER) cc_final: 0.5921 (mp10) REVERT: F 224 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7896 (pp) REVERT: F 344 PHE cc_start: 0.7432 (m-80) cc_final: 0.7123 (m-80) outliers start: 52 outliers final: 45 residues processed: 295 average time/residue: 0.3478 time to fit residues: 158.3436 Evaluate side-chains 300 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 249 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ASN 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 358 LYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 364 SER 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 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 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 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 533 ASN Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 73 GLN 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 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 450 VAL Chi-restraints excluded: chain E residue 607 LEU Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain F residue 116 GLN Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 47 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 69 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 171 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 173 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 183 optimal weight: 0.0970 chunk 194 optimal weight: 6.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.184027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.139841 restraints weight = 59543.447| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 3.66 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21256 Z= 0.118 Angle : 0.526 10.223 28904 Z= 0.264 Chirality : 0.038 0.173 3175 Planarity : 0.004 0.053 3584 Dihedral : 10.260 72.959 3285 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.64 % Allowed : 25.94 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.17), residues: 2466 helix: 1.81 (0.16), residues: 1127 sheet: 0.64 (0.33), residues: 232 loop : -1.49 (0.17), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 317 HIS 0.002 0.000 HIS B 605 PHE 0.013 0.001 PHE E 381 TYR 0.019 0.001 TYR F 253 ARG 0.007 0.000 ARG F 249 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 978) hydrogen bonds : angle 4.03159 ( 2720) covalent geometry : bond 0.00277 (21256) covalent geometry : angle 0.52639 (28904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8580.74 seconds wall clock time: 151 minutes 7.10 seconds (9067.10 seconds total)