Starting phenix.real_space_refine on Mon Aug 25 12:38:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y7m_39020/08_2025/8y7m_39020.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y7m_39020/08_2025/8y7m_39020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y7m_39020/08_2025/8y7m_39020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y7m_39020/08_2025/8y7m_39020.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y7m_39020/08_2025/8y7m_39020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y7m_39020/08_2025/8y7m_39020.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4064 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 185 5.16 5 C 15815 2.51 5 N 4294 2.21 5 O 4712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25006 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4032 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 26, 'TRANS': 479} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'PHE:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 39 Chain: "F" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4688 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 28, 'TRANS': 565} Chain breaks: 3 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 33 Chain: "G" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 641 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 5779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5779 Classifications: {'peptide': 712} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 30, 'TRANS': 681} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 5457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5457 Classifications: {'peptide': 686} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 655} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2463 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 13, 'TRANS': 294} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "I" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 975 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "J" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 971 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 5.50, per 1000 atoms: 0.22 Number of scatterers: 25006 At special positions: 0 Unit cell: (179.78, 177.11, 146.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 185 16.00 O 4712 8.00 N 4294 7.00 C 15815 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5884 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 24 sheets defined 53.3% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'E' and resid 209 through 217 Processing helix chain 'E' and resid 225 through 235 removed outlier: 4.145A pdb=" N PHE E 229 " --> pdb=" O CYS E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 249 Processing helix chain 'E' and resid 302 through 312 Processing helix chain 'E' and resid 330 through 347 removed outlier: 3.894A pdb=" N TYR E 334 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 371 Processing helix chain 'E' and resid 383 through 387 removed outlier: 4.070A pdb=" N ASP E 386 " --> pdb=" O ASN E 383 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL E 387 " --> pdb=" O CYS E 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 383 through 387' Processing helix chain 'E' and resid 405 through 415 removed outlier: 3.619A pdb=" N ASN E 409 " --> pdb=" O SER E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 451 Processing helix chain 'E' and resid 453 through 476 removed outlier: 4.215A pdb=" N GLU E 457 " --> pdb=" O CYS E 453 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR E 458 " --> pdb=" O ARG E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 537 removed outlier: 3.600A pdb=" N LYS E 536 " --> pdb=" O GLU E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 579 removed outlier: 3.807A pdb=" N LYS E 576 " --> pdb=" O LYS E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 582 through 603 removed outlier: 3.726A pdb=" N LYS E 603 " --> pdb=" O GLU E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 613 removed outlier: 3.529A pdb=" N GLU E 613 " --> pdb=" O LYS E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 650 Processing helix chain 'E' and resid 652 through 674 removed outlier: 3.765A pdb=" N GLU E 656 " --> pdb=" O SER E 652 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP E 674 " --> pdb=" O GLN E 670 " (cutoff:3.500A) Processing helix chain 'E' and resid 682 through 693 removed outlier: 4.641A pdb=" N LEU E 686 " --> pdb=" O ASP E 682 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR E 687 " --> pdb=" O LEU E 683 " (cutoff:3.500A) Processing helix chain 'E' and resid 697 through 714 removed outlier: 3.524A pdb=" N LEU E 701 " --> pdb=" O ASP E 697 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 12 Processing helix chain 'F' and resid 17 through 22 removed outlier: 3.642A pdb=" N PHE F 22 " --> pdb=" O SER F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 49 removed outlier: 3.717A pdb=" N GLN F 48 " --> pdb=" O ASN F 44 " (cutoff:3.500A) removed outlier: 3.876A 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 116 Processing helix chain 'F' and resid 118 through 124 removed outlier: 4.005A pdb=" N ARG F 121 " --> pdb=" O ARG F 118 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN F 124 " --> pdb=" O ARG F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 152 removed outlier: 3.528A pdb=" N SER F 152 " --> pdb=" O GLU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 161 removed outlier: 4.129A pdb=" N SER F 160 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY F 161 " --> pdb=" O ASN F 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 157 through 161' Processing helix chain 'F' and resid 163 through 176 Processing helix chain 'F' and resid 213 through 221 Processing helix chain 'F' and resid 248 through 264 Processing helix chain 'F' and resid 275 through 290 removed outlier: 3.759A pdb=" N LYS F 279 " --> pdb=" O GLY F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 313 removed outlier: 3.522A pdb=" N ASN F 312 " --> pdb=" O TRP F 309 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN F 313 " --> pdb=" O ASN F 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 309 through 313' Processing helix chain 'F' and resid 314 through 326 removed outlier: 3.645A pdb=" N PHE F 318 " --> pdb=" O ASN F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 345 removed outlier: 5.163A 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 372 through 376 removed outlier: 3.709A pdb=" N SER F 375 " --> pdb=" O MET F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 393 Processing helix chain 'F' and resid 415 through 426 removed outlier: 3.705A pdb=" N LEU F 419 " --> pdb=" O LEU F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 433 removed outlier: 3.717A pdb=" N LYS F 433 " --> pdb=" O LYS F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 474 Processing helix chain 'F' and resid 520 through 537 removed outlier: 4.569A 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: 3.532A pdb=" N GLY F 588 " --> pdb=" O SER F 585 " (cutoff:3.500A) removed outlier: 3.595A 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 removed outlier: 3.714A pdb=" N GLY F 594 " --> pdb=" O VAL F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 604 removed outlier: 3.722A pdb=" N LEU F 604 " --> pdb=" O ILE F 601 " (cutoff:3.500A) Processing helix chain 'F' and resid 607 through 613 Processing helix chain 'F' and resid 614 through 616 No H-bonds generated for 'chain 'F' and resid 614 through 616' Processing helix chain 'F' and resid 617 through 625 Processing helix chain 'G' and resid 46 through 51 removed outlier: 3.849A pdb=" N MET G 50 " --> pdb=" O ARG G 46 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET G 51 " --> pdb=" O MET G 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 46 through 51' Processing helix chain 'G' and resid 62 through 67 removed outlier: 3.742A pdb=" N MET G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 102 removed outlier: 3.807A pdb=" N VAL G 96 " --> pdb=" O SER G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 115 through 126 removed outlier: 3.795A pdb=" N PHE G 119 " --> pdb=" O TYR G 115 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU G 120 " --> pdb=" O LYS G 116 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS G 121 " --> pdb=" O THR G 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 10 through 25 removed outlier: 3.854A pdb=" N LEU A 16 " --> pdb=" O MET A 12 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 17 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 49 removed outlier: 3.768A pdb=" N SER A 49 " --> pdb=" O CYS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.956A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 184 Processing helix chain 'A' and resid 187 through 193 Processing helix chain 'A' and resid 209 through 217 removed outlier: 3.559A pdb=" N GLN A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 248 Processing helix chain 'A' and resid 302 through 313 removed outlier: 3.714A pdb=" N THR A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 347 removed outlier: 3.993A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 363 through 371 Processing helix chain 'A' and resid 405 through 414 removed outlier: 3.809A pdb=" N ASN A 409 " --> pdb=" O SER 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: 3.887A pdb=" N GLU A 457 " --> pdb=" O CYS A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 removed outlier: 3.764A pdb=" N LYS A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 603 removed outlier: 3.978A pdb=" N VAL A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 613 removed outlier: 3.609A pdb=" N PHE A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.728A pdb=" N GLU A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 693 removed outlier: 4.170A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 715 removed outlier: 3.686A pdb=" N HIS A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 removed outlier: 3.600A pdb=" N LYS B 11 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 21 removed outlier: 4.002A pdb=" N ILE B 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.912A pdb=" N THR B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET B 40 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 removed outlier: 4.073A pdb=" N ASN B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER B 106 " --> pdb=" O ILE B 102 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS B 107 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.639A pdb=" N ARG B 121 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 122 " --> pdb=" O VAL B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 removed outlier: 3.515A pdb=" N ASN B 153 " --> pdb=" O VAL B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.882A pdb=" N SER B 160 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 174 Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 248 through 264 removed outlier: 3.827A pdb=" N PHE B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 290 removed outlier: 3.517A pdb=" N VAL B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.687A pdb=" N ASN B 312 " --> pdb=" O TRP B 309 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 313 " --> pdb=" O ASN B 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 309 through 313' Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.557A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.769A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.853A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 removed outlier: 3.501A pdb=" N VAL B 418 " --> pdb=" O MET B 414 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 424 " --> pdb=" O GLY B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 474 removed outlier: 3.569A pdb=" N VAL B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 536 removed outlier: 4.525A pdb=" N SER B 524 " --> pdb=" O SER B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 560 removed outlier: 3.552A pdb=" N GLN B 545 " --> pdb=" O PRO B 541 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET B 546 " --> pdb=" O ALA B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 583 removed outlier: 3.541A pdb=" N LEU B 576 " --> pdb=" O ARG B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 594 removed outlier: 3.772A pdb=" N GLY B 594 " --> pdb=" O VAL B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.688A pdb=" N ASN B 603 " --> pdb=" O ASN B 600 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 604 " --> pdb=" O ILE B 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 600 through 604' Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 614 through 616 No H-bonds generated for 'chain 'B' and resid 614 through 616' Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 687 through 698 removed outlier: 3.716A pdb=" N LYS B 691 " --> pdb=" O GLN B 687 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS B 692 " --> pdb=" O MET B 688 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU B 697 " --> pdb=" O CYS B 693 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 705 removed outlier: 3.706A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 732 removed outlier: 3.713A pdb=" N ALA B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 755 removed outlier: 3.799A pdb=" N ALA B 741 " --> pdb=" O LYS B 737 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.814A pdb=" N ASN C 9 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU C 10 " --> pdb=" O GLU C 6 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 removed outlier: 3.674A pdb=" N ILE C 19 " --> pdb=" O ARG C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 60 through 66 removed outlier: 3.598A pdb=" N ILE C 63 " --> pdb=" O ASP C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 102 removed outlier: 3.815A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 removed outlier: 4.124A pdb=" N LYS C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL C 122 " --> pdb=" O TYR C 118 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU C 123 " --> pdb=" O PHE C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 168 removed outlier: 4.138A pdb=" N GLN C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 193 removed outlier: 3.826A pdb=" N LYS C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.564A pdb=" N ILE C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 225 through 230' Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.680A pdb=" N GLN C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 713 Processing helix chain 'C' and resid 744 through 754 removed outlier: 3.624A pdb=" N ALA C 750 " --> pdb=" O SER C 747 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 18 removed outlier: 3.563A pdb=" N GLN I 10 " --> pdb=" O VAL I 6 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS I 18 " --> pdb=" O LEU I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 89 removed outlier: 3.845A pdb=" N ILE I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR I 33 " --> pdb=" O ASN I 29 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN I 34 " --> pdb=" O GLY I 30 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU I 36 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU I 47 " --> pdb=" O ASP I 43 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA I 48 " --> pdb=" O SER I 44 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET I 52 " --> pdb=" O ALA I 48 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY I 53 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ASP I 54 " --> pdb=" O MET I 50 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU I 55 " --> pdb=" O ARG I 51 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS I 56 " --> pdb=" O MET I 52 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY I 63 " --> pdb=" O GLN I 59 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS I 64 " --> pdb=" O ASN I 60 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TRP I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG I 66 " --> pdb=" O ASN I 62 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU I 67 " --> pdb=" O GLY I 63 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY I 70 " --> pdb=" O ARG I 66 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN I 71 " --> pdb=" O GLU I 67 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU I 74 " --> pdb=" O GLY I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 121 removed outlier: 3.811A pdb=" N ILE I 121 " --> pdb=" O SER I 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 22 removed outlier: 3.713A pdb=" N GLY J 22 " --> pdb=" O LYS J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 50 Processing helix chain 'J' and resid 54 through 59 removed outlier: 3.500A pdb=" N LEU J 58 " --> pdb=" O ASP J 54 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN J 59 " --> pdb=" O LEU J 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 54 through 59' Processing helix chain 'J' and resid 63 through 66 Processing helix chain 'J' and resid 67 through 90 removed outlier: 3.871A pdb=" N GLN J 71 " --> pdb=" O GLU J 67 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU J 75 " --> pdb=" O GLN J 71 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG J 77 " --> pdb=" O PHE J 73 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TRP J 78 " --> pdb=" O GLU J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 121 Processing sheet with id=AA1, first strand: chain 'E' and resid 258 through 259 removed outlier: 6.081A pdb=" N LYS F 481 " --> pdb=" O ASP F 305 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP F 305 " --> pdb=" O LYS F 481 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR F 483 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR F 303 " --> pdb=" O TYR F 483 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY F 304 " --> pdb=" O PHE F 447 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE F 447 " --> pdb=" O GLY F 304 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP F 437 " --> pdb=" O ASN F 452 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 317 through 324 removed outlier: 9.942A pdb=" N TRP E 317 " --> pdb=" O MET E 548 " (cutoff:3.500A) removed outlier: 9.383A pdb=" N MET E 548 " --> pdb=" O TRP E 317 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU E 319 " --> pdb=" O GLY E 546 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLY E 546 " --> pdb=" O GLU E 319 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR E 321 " --> pdb=" O GLU E 544 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL E 542 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N VAL E 542 " --> pdb=" O VAL E 565 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL E 565 " --> pdb=" O VAL E 542 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLU E 544 " --> pdb=" O LEU E 563 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU E 563 " --> pdb=" O GLU E 544 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY E 546 " --> pdb=" O MET E 561 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N TYR E 501 " --> pdb=" O PHE E 525 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N MET E 485 " --> pdb=" O TYR E 501 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N PHE E 503 " --> pdb=" O ILE E 483 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE E 483 " --> pdb=" O PHE E 503 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE E 505 " --> pdb=" O GLN E 481 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLN E 481 " --> pdb=" O ILE E 505 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 390 through 391 removed outlier: 4.134A pdb=" N LYS E 391 " --> pdb=" O GLU F 358 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU F 358 " --> pdb=" O LYS E 391 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR F 355 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE F 368 " --> pdb=" O TYR F 355 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 628 through 631 removed outlier: 3.838A pdb=" N GLY E 622 " --> pdb=" O GLU E 629 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLY E 631 " --> pdb=" O PRO E 620 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 55 through 57 Processing sheet with id=AA6, first strand: chain 'F' and resid 129 through 130 Processing sheet with id=AA7, first strand: chain 'F' and resid 223 through 224 Processing sheet with id=AA8, first strand: chain 'F' and resid 490 through 492 Processing sheet with id=AA9, first strand: chain 'G' and resid 57 through 59 removed outlier: 4.162A pdb=" N MET G 90 " --> pdb=" O SER G 79 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.511A pdb=" N PHE A 53 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 109 through 111 removed outlier: 3.523A pdb=" N ASP A 111 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A 116 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHE A 117 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.647A pdb=" N PHE B 447 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 317 through 324 removed outlier: 10.240A pdb=" N TRP A 317 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N MET A 548 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N GLU A 319 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY A 546 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A 542 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL A 542 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL A 565 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLU A 544 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU A 563 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY A 546 " --> pdb=" O MET A 561 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET A 557 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 525 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A 481 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 377 through 378 removed outlier: 5.833A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 364 " --> pdb=" O SER B 359 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU B 358 " --> pdb=" O LYS A 391 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 391 " --> pdb=" O GLU B 358 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.854A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 621 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AB8, first strand: chain 'B' and resid 128 through 130 removed outlier: 3.589A pdb=" N ARG B 135 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 179 through 183 Processing sheet with id=AC1, first strand: chain 'B' and resid 223 through 224 Processing sheet with id=AC2, first strand: chain 'B' and resid 490 through 491 Processing sheet with id=AC3, first strand: chain 'C' and resid 57 through 59 removed outlier: 3.850A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 129 through 135 removed outlier: 5.804A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C 245 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET C 243 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 143 through 148 removed outlier: 3.802A pdb=" N ARG C 143 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU C 218 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 147 " --> pdb=" O LYS C 214 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 694 through 699 removed outlier: 3.557A pdb=" N LEU C 695 " --> pdb=" O MET C 735 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET C 735 " --> pdb=" O LEU C 695 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU C 733 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LYS C 699 " --> pdb=" O VAL C 731 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL C 731 " --> pdb=" O LYS C 699 " (cutoff:3.500A) 1146 hydrogen bonds defined for protein. 3258 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.50 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6982 1.33 - 1.45: 4034 1.45 - 1.57: 14163 1.57 - 1.69: 2 1.69 - 1.81: 323 Bond restraints: 25504 Sorted by residual: bond pdb=" CA GLU F 109 " pdb=" C GLU F 109 " ideal model delta sigma weight residual 1.524 1.585 -0.061 1.27e-02 6.20e+03 2.33e+01 bond pdb=" CA GLU A 293 " pdb=" C GLU A 293 " ideal model delta sigma weight residual 1.528 1.489 0.039 8.80e-03 1.29e+04 1.95e+01 bond pdb=" CA MET B 174 " pdb=" C MET B 174 " ideal model delta sigma weight residual 1.522 1.573 -0.051 1.72e-02 3.38e+03 8.84e+00 bond pdb=" N VAL I 6 " pdb=" CA VAL I 6 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.72e+00 bond pdb=" CA SER I 25 " pdb=" CB SER I 25 " ideal model delta sigma weight residual 1.532 1.492 0.039 1.36e-02 5.41e+03 8.39e+00 ... (remaining 25499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 34000 2.48 - 4.96: 371 4.96 - 7.44: 27 7.44 - 9.92: 2 9.92 - 12.40: 4 Bond angle restraints: 34404 Sorted by residual: angle pdb=" N ILE A 292 " pdb=" CA ILE A 292 " pdb=" C ILE A 292 " ideal model delta sigma weight residual 112.83 100.60 12.23 9.90e-01 1.02e+00 1.53e+02 angle pdb=" N THR F 110 " pdb=" CA THR F 110 " pdb=" C THR F 110 " ideal model delta sigma weight residual 111.33 122.64 -11.31 1.21e+00 6.83e-01 8.74e+01 angle pdb=" C VAL J 49 " pdb=" N MET J 50 " pdb=" CA MET J 50 " ideal model delta sigma weight residual 122.31 109.91 12.40 2.00e+00 2.50e-01 3.84e+01 angle pdb=" N ASN I 29 " pdb=" CA ASN I 29 " pdb=" C ASN I 29 " ideal model delta sigma weight residual 113.50 105.95 7.55 1.23e+00 6.61e-01 3.77e+01 angle pdb=" N ASP A 294 " pdb=" CA ASP A 294 " pdb=" C ASP A 294 " ideal model delta sigma weight residual 109.65 117.08 -7.43 1.26e+00 6.30e-01 3.48e+01 ... (remaining 34399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 14023 17.56 - 35.13: 1287 35.13 - 52.69: 201 52.69 - 70.25: 44 70.25 - 87.81: 17 Dihedral angle restraints: 15572 sinusoidal: 6492 harmonic: 9080 Sorted by residual: dihedral pdb=" N GLU F 109 " pdb=" C GLU F 109 " pdb=" CA GLU F 109 " pdb=" CB GLU F 109 " ideal model delta harmonic sigma weight residual 122.80 134.98 -12.18 0 2.50e+00 1.60e-01 2.37e+01 dihedral pdb=" C GLU F 109 " pdb=" N GLU F 109 " pdb=" CA GLU F 109 " pdb=" CB GLU F 109 " ideal model delta harmonic sigma weight residual -122.60 -134.38 11.78 0 2.50e+00 1.60e-01 2.22e+01 dihedral pdb=" CA SER A 571 " pdb=" C SER A 571 " pdb=" N LYS A 572 " pdb=" CA LYS A 572 " ideal model delta harmonic sigma weight residual 180.00 158.15 21.85 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 15569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3531 0.083 - 0.166: 229 0.166 - 0.249: 7 0.249 - 0.332: 1 0.332 - 0.416: 1 Chirality restraints: 3769 Sorted by residual: chirality pdb=" CA GLU F 109 " pdb=" N GLU F 109 " pdb=" C GLU F 109 " pdb=" CB GLU F 109 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" CA THR F 110 " pdb=" N THR F 110 " pdb=" C THR F 110 " pdb=" CB THR F 110 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA ASP A 294 " pdb=" N ASP A 294 " pdb=" C ASP A 294 " pdb=" CB ASP A 294 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 3766 not shown) Planarity restraints: 4428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 109 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.33e+00 pdb=" C GLU F 109 " -0.050 2.00e-02 2.50e+03 pdb=" O GLU F 109 " 0.020 2.00e-02 2.50e+03 pdb=" N THR F 110 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 437 " 0.018 2.00e-02 2.50e+03 1.64e-02 6.73e+00 pdb=" CG TRP B 437 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP B 437 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 437 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 437 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 437 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 437 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 437 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 437 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 437 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 624 " -0.042 5.00e-02 4.00e+02 6.26e-02 6.28e+00 pdb=" N PRO E 625 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 625 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 625 " -0.035 5.00e-02 4.00e+02 ... (remaining 4425 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3894 2.76 - 3.29: 23228 3.29 - 3.83: 38267 3.83 - 4.36: 43433 4.36 - 4.90: 77287 Nonbonded interactions: 186109 Sorted by model distance: nonbonded pdb=" O LEU F 378 " pdb=" NH1 ARG F 386 " model vdw 2.225 3.120 nonbonded pdb=" O ASN G 102 " pdb=" ND2 ASN G 102 " model vdw 2.231 3.120 nonbonded pdb=" O ARG F 563 " pdb=" OG1 THR F 566 " model vdw 2.245 3.040 nonbonded pdb=" O SER F 269 " pdb=" NZ LYS F 281 " model vdw 2.246 3.120 nonbonded pdb=" NH2 ARG E 583 " pdb=" O LEU F 509 " model vdw 2.257 3.120 ... (remaining 186104 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 'B' and (resid 1 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 44 or (resid 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 through 64 or (resid 65 and (n \ ame N or name CA or name C or name O or name CB )) or resid 66 through 179 or re \ sid 211 through 226 or resid 244 through 429 or (resid 430 and (name N or name C \ A or name C or name O or name CB )) or resid 431 through 506 or (resid 507 and ( \ name N or name CA or name C or name O or name CB )) or resid 508 through 583 or \ (resid 584 and (name N or name CA or name C or name O or name CB )) or resid 585 \ through 632 or resid 662 through 671)) selection = (chain 'F' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 671)) } ncs_group { reference = (chain 'I' and (resid 5 through 58 or (resid 59 and (name N or name CA or name C \ or name O or name CB )) or resid 60 through 121)) selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 19.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 22.790 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 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 0.061 25504 Z= 0.167 Angle : 0.638 12.395 34404 Z= 0.368 Chirality : 0.043 0.416 3769 Planarity : 0.005 0.063 4428 Dihedral : 13.685 87.814 9688 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.04 % Favored : 93.83 % Rotamer: Outliers : 0.22 % Allowed : 0.40 % Favored : 99.38 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.15), residues: 3077 helix: 0.93 (0.14), residues: 1506 sheet: 0.10 (0.35), residues: 222 loop : -2.20 (0.15), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 737 TYR 0.016 0.001 TYR F 30 PHE 0.027 0.001 PHE B 512 TRP 0.044 0.002 TRP B 437 HIS 0.003 0.001 HIS F 47 Details of bonding type rmsd covalent geometry : bond 0.00317 (25504) covalent geometry : angle 0.63837 (34404) hydrogen bonds : bond 0.18252 ( 1146) hydrogen bonds : angle 5.40832 ( 3258) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 790 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 238 PRO cc_start: 0.7592 (Cg_endo) cc_final: 0.7200 (Cg_exo) REVERT: E 286 ASP cc_start: 0.8061 (m-30) cc_final: 0.7825 (m-30) REVERT: E 347 ASP cc_start: 0.6874 (t70) cc_final: 0.6672 (t70) REVERT: E 670 GLN cc_start: 0.8331 (tp40) cc_final: 0.7959 (tp40) REVERT: E 676 LEU cc_start: 0.7570 (mt) cc_final: 0.7263 (mt) REVERT: F 104 GLU cc_start: 0.5912 (mp0) cc_final: 0.5513 (mp0) REVERT: F 120 ASP cc_start: 0.5582 (p0) cc_final: 0.5242 (p0) REVERT: F 130 ASP cc_start: 0.7635 (t0) cc_final: 0.7356 (t0) REVERT: F 168 LYS cc_start: 0.8306 (ptmt) cc_final: 0.8066 (ptmt) REVERT: F 260 ARG cc_start: 0.7370 (mtp-110) cc_final: 0.7093 (mtp-110) REVERT: F 395 LEU cc_start: 0.7701 (tt) cc_final: 0.7430 (mp) REVERT: F 398 ASP cc_start: 0.6053 (p0) cc_final: 0.5845 (p0) REVERT: F 431 TYR cc_start: 0.6913 (m-10) cc_final: 0.6618 (m-10) REVERT: F 475 ILE cc_start: 0.8001 (pt) cc_final: 0.7792 (mp) REVERT: F 614 GLU cc_start: 0.7019 (pp20) cc_final: 0.6652 (pp20) REVERT: F 632 VAL cc_start: 0.8156 (t) cc_final: 0.7407 (t) REVERT: A 95 CYS cc_start: 0.6624 (p) cc_final: 0.5984 (t) REVERT: A 114 GLU cc_start: 0.7806 (tp30) cc_final: 0.7541 (tp30) REVERT: A 127 VAL cc_start: 0.8301 (t) cc_final: 0.8074 (p) REVERT: A 173 THR cc_start: 0.7900 (m) cc_final: 0.7532 (p) REVERT: A 214 LEU cc_start: 0.7925 (mt) cc_final: 0.7600 (mt) REVERT: A 508 ARG cc_start: 0.6758 (mtt90) cc_final: 0.5943 (mtt-85) REVERT: A 692 GLU cc_start: 0.6827 (pp20) cc_final: 0.6579 (tm-30) REVERT: A 712 THR cc_start: 0.8438 (t) cc_final: 0.8225 (m) REVERT: B 441 LEU cc_start: 0.8509 (pp) cc_final: 0.8216 (pt) REVERT: B 557 TYR cc_start: 0.7500 (t80) cc_final: 0.7158 (t80) REVERT: B 742 GLU cc_start: 0.7329 (tp30) cc_final: 0.6922 (tp30) REVERT: C 49 TRP cc_start: 0.6247 (m-10) cc_final: 0.6035 (m-10) REVERT: C 214 LYS cc_start: 0.7313 (pttp) cc_final: 0.7075 (pttp) REVERT: I 13 LEU cc_start: 0.8540 (mt) cc_final: 0.8253 (mt) REVERT: I 26 GLU cc_start: 0.6213 (OUTLIER) cc_final: 0.5999 (tm-30) REVERT: I 40 LEU cc_start: 0.7240 (mp) cc_final: 0.6187 (mp) REVERT: I 107 PHE cc_start: 0.7636 (m-10) cc_final: 0.7362 (m-10) REVERT: I 108 GLU cc_start: 0.6945 (tt0) cc_final: 0.6615 (tt0) outliers start: 6 outliers final: 2 residues processed: 794 average time/residue: 0.6354 time to fit residues: 573.7045 Evaluate side-chains 644 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 641 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 355 TYR Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 69 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 197 optimal weight: 0.0270 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.8980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 GLN E 350 ASN E 408 GLN E 412 ASN E 452 HIS E 499 ASN F 124 GLN F 335 ASN F 476 ASN F 569 GLN F 603 ASN G 102 ASN A 136 ASN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN A 471 ASN B 58 ASN B 116 GLN B 145 ASN B 184 HIS B 335 ASN ** B 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 ASN C 27 HIS I 20 GLN J 104 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.123595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.101041 restraints weight = 38082.335| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.07 r_work: 0.3127 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 25504 Z= 0.200 Angle : 0.703 9.830 34404 Z= 0.369 Chirality : 0.045 0.208 3769 Planarity : 0.005 0.066 4428 Dihedral : 5.287 60.186 3392 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.56 % Favored : 93.31 % Rotamer: Outliers : 3.12 % Allowed : 15.26 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.15), residues: 3077 helix: 1.04 (0.14), residues: 1516 sheet: 0.49 (0.35), residues: 214 loop : -2.30 (0.15), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 269 TYR 0.020 0.002 TYR A 48 PHE 0.023 0.002 PHE B 512 TRP 0.033 0.002 TRP B 437 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00455 (25504) covalent geometry : angle 0.70277 (34404) hydrogen bonds : bond 0.07589 ( 1146) hydrogen bonds : angle 4.30295 ( 3258) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 683 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 262 LYS cc_start: 0.8865 (ttmm) cc_final: 0.8493 (ttpp) REVERT: E 263 THR cc_start: 0.8676 (m) cc_final: 0.8469 (p) REVERT: E 347 ASP cc_start: 0.8043 (t70) cc_final: 0.7836 (t70) REVERT: E 512 ARG cc_start: 0.8344 (mtp85) cc_final: 0.7970 (mtp85) REVERT: E 544 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: E 673 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8103 (mtt-85) REVERT: F 104 GLU cc_start: 0.7409 (mp0) cc_final: 0.6845 (mp0) REVERT: F 106 SER cc_start: 0.8749 (OUTLIER) cc_final: 0.8389 (m) REVERT: F 130 ASP cc_start: 0.7650 (t0) cc_final: 0.7415 (t0) REVERT: F 141 THR cc_start: 0.8382 (p) cc_final: 0.8178 (t) REVERT: F 158 ASN cc_start: 0.8007 (t0) cc_final: 0.7777 (t0) REVERT: F 387 LYS cc_start: 0.8065 (tttp) cc_final: 0.7831 (tttp) REVERT: F 398 ASP cc_start: 0.7814 (p0) cc_final: 0.7495 (p0) REVERT: F 475 ILE cc_start: 0.8120 (pt) cc_final: 0.7842 (mt) REVERT: F 528 THR cc_start: 0.8689 (t) cc_final: 0.8428 (m) REVERT: F 614 GLU cc_start: 0.7839 (pp20) cc_final: 0.7528 (pp20) REVERT: F 616 MET cc_start: 0.8631 (ptm) cc_final: 0.8417 (ptp) REVERT: G 102 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8510 (p0) REVERT: A 7 GLN cc_start: 0.8048 (pp30) cc_final: 0.7569 (pp30) REVERT: A 18 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: A 19 LYS cc_start: 0.8301 (mttt) cc_final: 0.8028 (mttt) REVERT: A 50 ASP cc_start: 0.7582 (t0) cc_final: 0.6821 (t0) REVERT: A 51 PHE cc_start: 0.7692 (m-80) cc_final: 0.7379 (m-80) REVERT: A 95 CYS cc_start: 0.7171 (p) cc_final: 0.6658 (t) REVERT: A 114 GLU cc_start: 0.8183 (tp30) cc_final: 0.7738 (tp30) REVERT: A 122 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8751 (t) REVERT: A 129 ILE cc_start: 0.8699 (mm) cc_final: 0.8081 (mm) REVERT: A 133 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7091 (mp0) REVERT: A 148 PHE cc_start: 0.8595 (m-10) cc_final: 0.7888 (m-80) REVERT: A 327 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6798 (pm20) REVERT: A 382 ASP cc_start: 0.8158 (p0) cc_final: 0.7765 (p0) REVERT: A 693 CYS cc_start: 0.7342 (t) cc_final: 0.7127 (t) REVERT: B 169 ASP cc_start: 0.8217 (t70) cc_final: 0.7991 (t0) REVERT: B 264 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8190 (mt-10) REVERT: B 267 GLU cc_start: 0.7653 (pm20) cc_final: 0.7436 (pm20) REVERT: B 435 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8510 (m) REVERT: B 481 LYS cc_start: 0.8361 (mtmm) cc_final: 0.8136 (mtmm) REVERT: B 557 TYR cc_start: 0.8341 (t80) cc_final: 0.8101 (t80) REVERT: B 694 ASN cc_start: 0.8141 (m110) cc_final: 0.7928 (m110) REVERT: B 699 PHE cc_start: 0.8486 (m-80) cc_final: 0.8131 (m-80) REVERT: B 751 GLU cc_start: 0.7802 (tt0) cc_final: 0.7556 (tt0) REVERT: C 46 ARG cc_start: 0.8142 (ttp-170) cc_final: 0.7879 (ttp-170) REVERT: C 47 MET cc_start: 0.8650 (tpt) cc_final: 0.8432 (tpt) REVERT: C 49 TRP cc_start: 0.7154 (m-10) cc_final: 0.6912 (m-10) REVERT: C 171 GLU cc_start: 0.7979 (tt0) cc_final: 0.7743 (mt-10) REVERT: C 176 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7520 (tt) REVERT: C 733 LEU cc_start: 0.7623 (mp) cc_final: 0.7181 (mp) REVERT: C 756 MET cc_start: 0.4155 (mpm) cc_final: 0.3915 (mpm) REVERT: I 26 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6647 (tm-30) REVERT: I 74 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7011 (mm-30) REVERT: I 75 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7216 (mm-30) REVERT: I 106 LEU cc_start: 0.7661 (mp) cc_final: 0.7460 (tp) REVERT: J 50 MET cc_start: 0.4192 (pmm) cc_final: 0.3989 (pmm) REVERT: J 65 TRP cc_start: 0.6425 (t60) cc_final: 0.6138 (t60) outliers start: 86 outliers final: 25 residues processed: 711 average time/residue: 0.7284 time to fit residues: 582.0971 Evaluate side-chains 663 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 627 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain E residue 544 GLU Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 673 ARG Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 171 MET Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 267 GLU Chi-restraints excluded: chain F residue 409 MET Chi-restraints excluded: chain F residue 534 MET Chi-restraints excluded: chain F residue 618 GLU Chi-restraints excluded: chain F residue 662 THR Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain J residue 105 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 234 optimal weight: 0.8980 chunk 208 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 112 optimal weight: 2.9990 chunk 295 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 302 optimal weight: 0.2980 chunk 143 optimal weight: 0.7980 chunk 287 optimal weight: 0.7980 chunk 282 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 217 GLN E 452 HIS F 284 ASN F 603 ASN A 136 ASN B 134 ASN B 518 ASN B 533 ASN C 110 HIS I 29 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.121144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.098223 restraints weight = 38129.493| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.12 r_work: 0.3080 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25504 Z= 0.181 Angle : 0.632 11.629 34404 Z= 0.336 Chirality : 0.043 0.227 3769 Planarity : 0.005 0.060 4428 Dihedral : 4.945 55.729 3388 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.82 % Favored : 94.02 % Rotamer: Outliers : 3.71 % Allowed : 19.11 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.15), residues: 3077 helix: 1.15 (0.14), residues: 1537 sheet: 0.50 (0.34), residues: 228 loop : -2.38 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 170 TYR 0.017 0.002 TYR F 30 PHE 0.042 0.002 PHE B 512 TRP 0.017 0.002 TRP B 437 HIS 0.004 0.001 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00418 (25504) covalent geometry : angle 0.63172 (34404) hydrogen bonds : bond 0.07436 ( 1146) hydrogen bonds : angle 4.25031 ( 3258) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 645 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 262 LYS cc_start: 0.8794 (ttmm) cc_final: 0.8543 (ttpp) REVERT: E 347 ASP cc_start: 0.8095 (t70) cc_final: 0.7799 (t0) REVERT: E 430 GLU cc_start: 0.7645 (pm20) cc_final: 0.7394 (pm20) REVERT: E 512 ARG cc_start: 0.8334 (mtp85) cc_final: 0.7976 (mtp85) REVERT: E 544 GLU cc_start: 0.8187 (tt0) cc_final: 0.7913 (tt0) REVERT: E 667 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8222 (mt) REVERT: E 673 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8005 (mtt-85) REVERT: F 78 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8051 (mm-30) REVERT: F 104 GLU cc_start: 0.7530 (mp0) cc_final: 0.7059 (mp0) REVERT: F 158 ASN cc_start: 0.8009 (t0) cc_final: 0.7782 (t0) REVERT: F 398 ASP cc_start: 0.7933 (p0) cc_final: 0.7601 (p0) REVERT: F 442 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: F 475 ILE cc_start: 0.8278 (pt) cc_final: 0.7875 (mt) REVERT: F 614 GLU cc_start: 0.7942 (pp20) cc_final: 0.7574 (pp20) REVERT: G 102 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.8345 (p0) REVERT: A 7 GLN cc_start: 0.8088 (pp30) cc_final: 0.7737 (pp30) REVERT: A 18 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: A 19 LYS cc_start: 0.8467 (mttt) cc_final: 0.8133 (mttt) REVERT: A 34 LYS cc_start: 0.7638 (mtpp) cc_final: 0.7348 (mttm) REVERT: A 95 CYS cc_start: 0.7025 (p) cc_final: 0.6633 (t) REVERT: A 114 GLU cc_start: 0.8267 (tp30) cc_final: 0.7727 (tp30) REVERT: A 122 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8743 (t) REVERT: A 129 ILE cc_start: 0.8686 (mm) cc_final: 0.8464 (mm) REVERT: A 133 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7453 (mp0) REVERT: A 148 PHE cc_start: 0.8801 (m-10) cc_final: 0.8374 (m-80) REVERT: A 163 LEU cc_start: 0.8083 (mt) cc_final: 0.7866 (mt) REVERT: A 199 GLU cc_start: 0.7880 (pm20) cc_final: 0.7659 (pm20) REVERT: A 327 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6906 (pm20) REVERT: A 374 MET cc_start: 0.7067 (mpp) cc_final: 0.6796 (mpp) REVERT: A 385 ARG cc_start: 0.8387 (ttp-110) cc_final: 0.8100 (ttm-80) REVERT: A 469 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8726 (tt) REVERT: A 548 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8120 (ttm) REVERT: A 691 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: A 693 CYS cc_start: 0.7491 (t) cc_final: 0.7190 (t) REVERT: A 712 THR cc_start: 0.8625 (t) cc_final: 0.8364 (m) REVERT: B 169 ASP cc_start: 0.8246 (t70) cc_final: 0.8038 (t0) REVERT: B 178 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7200 (tp30) REVERT: B 180 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7784 (mp0) REVERT: B 212 VAL cc_start: 0.8267 (OUTLIER) cc_final: 0.7971 (m) REVERT: B 264 GLU cc_start: 0.8452 (tp30) cc_final: 0.8232 (mt-10) REVERT: B 267 GLU cc_start: 0.7760 (pm20) cc_final: 0.7518 (pm20) REVERT: B 319 LEU cc_start: 0.8372 (tp) cc_final: 0.8093 (tt) REVERT: B 371 GLU cc_start: 0.7796 (tp30) cc_final: 0.7515 (tp30) REVERT: B 386 ARG cc_start: 0.8080 (mtp-110) cc_final: 0.7476 (ttm-80) REVERT: B 403 LEU cc_start: 0.8761 (tp) cc_final: 0.8521 (tt) REVERT: B 435 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8618 (m) REVERT: B 481 LYS cc_start: 0.8553 (mtmm) cc_final: 0.8097 (mtmm) REVERT: B 557 TYR cc_start: 0.8282 (t80) cc_final: 0.8071 (t80) REVERT: B 667 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8540 (mp) REVERT: B 687 GLN cc_start: 0.7788 (mp10) cc_final: 0.7536 (mp10) REVERT: B 694 ASN cc_start: 0.8372 (m110) cc_final: 0.8143 (m110) REVERT: B 699 PHE cc_start: 0.8488 (m-80) cc_final: 0.8199 (m-80) REVERT: B 751 GLU cc_start: 0.7844 (tt0) cc_final: 0.7610 (tt0) REVERT: C 46 ARG cc_start: 0.8200 (ttp-170) cc_final: 0.7929 (ttp-170) REVERT: C 69 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: C 116 LYS cc_start: 0.8419 (ptmm) cc_final: 0.8107 (ptmm) REVERT: C 171 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7912 (mt-10) REVERT: C 177 LEU cc_start: 0.8392 (tt) cc_final: 0.8114 (tp) REVERT: C 735 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7605 (pp-130) REVERT: C 736 LYS cc_start: 0.8465 (tppp) cc_final: 0.8116 (tptm) REVERT: C 756 MET cc_start: 0.4277 (mpm) cc_final: 0.3467 (mpm) REVERT: I 26 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6559 (tm-30) REVERT: I 74 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7243 (mm-30) REVERT: I 100 MET cc_start: 0.6984 (mmp) cc_final: 0.6661 (mmp) REVERT: I 106 LEU cc_start: 0.7787 (mp) cc_final: 0.7414 (tp) REVERT: J 50 MET cc_start: 0.4429 (pmm) cc_final: 0.4196 (pmm) REVERT: J 65 TRP cc_start: 0.6622 (t60) cc_final: 0.6290 (t60) outliers start: 102 outliers final: 42 residues processed: 688 average time/residue: 0.7830 time to fit residues: 601.9869 Evaluate side-chains 699 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 639 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 673 ARG Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 267 GLU Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 305 ASP Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 432 THR Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 442 GLN Chi-restraints excluded: chain F residue 618 GLU Chi-restraints excluded: chain F residue 662 THR Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 735 MET Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 109 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 155 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 207 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 17 optimal weight: 0.0670 chunk 15 optimal weight: 0.5980 chunk 161 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 264 optimal weight: 0.1980 chunk 237 optimal weight: 0.0870 overall best weight: 0.2096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 713 HIS ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 ASN F 597 ASN F 603 ASN G 102 ASN A 92 ASN A 248 GLN B 134 ASN B 504 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.125960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.103309 restraints weight = 37910.997| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.08 r_work: 0.3150 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25504 Z= 0.117 Angle : 0.552 8.711 34404 Z= 0.292 Chirality : 0.040 0.187 3769 Planarity : 0.004 0.050 4428 Dihedral : 4.598 50.970 3388 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.82 % Favored : 94.09 % Rotamer: Outliers : 4.11 % Allowed : 20.68 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.15), residues: 3077 helix: 1.39 (0.14), residues: 1526 sheet: 0.31 (0.32), residues: 248 loop : -2.27 (0.15), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 486 TYR 0.017 0.001 TYR F 30 PHE 0.023 0.001 PHE B 512 TRP 0.012 0.001 TRP F 437 HIS 0.002 0.000 HIS E 452 Details of bonding type rmsd covalent geometry : bond 0.00248 (25504) covalent geometry : angle 0.55180 (34404) hydrogen bonds : bond 0.05095 ( 1146) hydrogen bonds : angle 3.99019 ( 3258) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 646 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 229 PHE cc_start: 0.6110 (m-80) cc_final: 0.4562 (t80) REVERT: E 262 LYS cc_start: 0.8671 (ttmm) cc_final: 0.8426 (ttpp) REVERT: E 321 TYR cc_start: 0.8809 (p90) cc_final: 0.8475 (p90) REVERT: E 347 ASP cc_start: 0.7853 (t70) cc_final: 0.7596 (t0) REVERT: E 430 GLU cc_start: 0.7636 (pm20) cc_final: 0.7382 (pm20) REVERT: E 478 ASP cc_start: 0.8321 (p0) cc_final: 0.8115 (p0) REVERT: E 512 ARG cc_start: 0.8199 (mtp85) cc_final: 0.7876 (mtp85) REVERT: E 544 GLU cc_start: 0.8106 (tt0) cc_final: 0.7829 (tt0) REVERT: E 691 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8026 (mt-10) REVERT: F 76 ASP cc_start: 0.7118 (p0) cc_final: 0.6897 (p0) REVERT: F 104 GLU cc_start: 0.7526 (mp0) cc_final: 0.7047 (mp0) REVERT: F 108 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8629 (mp) REVERT: F 148 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7283 (pp20) REVERT: F 158 ASN cc_start: 0.7955 (t0) cc_final: 0.7717 (t0) REVERT: F 260 ARG cc_start: 0.8484 (mtp-110) cc_final: 0.8228 (mmm-85) REVERT: F 398 ASP cc_start: 0.7964 (p0) cc_final: 0.7654 (p0) REVERT: F 409 MET cc_start: 0.6534 (OUTLIER) cc_final: 0.6252 (ptt) REVERT: F 442 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8159 (tt0) REVERT: F 475 ILE cc_start: 0.8171 (pt) cc_final: 0.7777 (mt) REVERT: F 502 VAL cc_start: 0.8233 (OUTLIER) cc_final: 0.7902 (t) REVERT: F 571 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7072 (ttp80) REVERT: F 614 GLU cc_start: 0.7943 (pp20) cc_final: 0.7642 (pp20) REVERT: G 102 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8347 (p0) REVERT: A 7 GLN cc_start: 0.8057 (pp30) cc_final: 0.7808 (pp30) REVERT: A 18 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: A 34 LYS cc_start: 0.7508 (mtpp) cc_final: 0.7218 (mttt) REVERT: A 65 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6261 (mm) REVERT: A 95 CYS cc_start: 0.7039 (p) cc_final: 0.6698 (t) REVERT: A 114 GLU cc_start: 0.8222 (tp30) cc_final: 0.7673 (tp30) REVERT: A 122 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8721 (t) REVERT: A 128 HIS cc_start: 0.7163 (m-70) cc_final: 0.6866 (m-70) REVERT: A 129 ILE cc_start: 0.8655 (mm) cc_final: 0.8119 (mm) REVERT: A 148 PHE cc_start: 0.8831 (m-10) cc_final: 0.8374 (m-80) REVERT: A 179 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8478 (tmt170) REVERT: A 181 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7594 (tm-30) REVERT: A 184 ASN cc_start: 0.8254 (t0) cc_final: 0.8030 (t0) REVERT: A 199 GLU cc_start: 0.7845 (pm20) cc_final: 0.7639 (pm20) REVERT: A 288 LEU cc_start: 0.7949 (pt) cc_final: 0.7602 (pt) REVERT: A 327 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6803 (pm20) REVERT: A 380 ASP cc_start: 0.7787 (t70) cc_final: 0.7355 (p0) REVERT: A 385 ARG cc_start: 0.8271 (ttp-110) cc_final: 0.8002 (ttm-80) REVERT: A 450 VAL cc_start: 0.8210 (OUTLIER) cc_final: 0.7987 (p) REVERT: A 469 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8635 (tt) REVERT: A 548 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.8110 (ttm) REVERT: A 691 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: A 693 CYS cc_start: 0.7379 (t) cc_final: 0.7094 (t) REVERT: B 96 GLU cc_start: 0.8383 (tp30) cc_final: 0.8019 (tp30) REVERT: B 169 ASP cc_start: 0.8237 (t70) cc_final: 0.8021 (t0) REVERT: B 178 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7304 (mm-30) REVERT: B 212 VAL cc_start: 0.8257 (t) cc_final: 0.7940 (m) REVERT: B 267 GLU cc_start: 0.7716 (pm20) cc_final: 0.7490 (pm20) REVERT: B 319 LEU cc_start: 0.8295 (tp) cc_final: 0.8054 (tt) REVERT: B 371 GLU cc_start: 0.7770 (tp30) cc_final: 0.7482 (tp30) REVERT: B 504 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.7941 (p0) REVERT: B 667 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8541 (mp) REVERT: B 687 GLN cc_start: 0.7784 (mp10) cc_final: 0.7556 (mp10) REVERT: B 694 ASN cc_start: 0.8361 (m110) cc_final: 0.8122 (m110) REVERT: B 699 PHE cc_start: 0.8473 (m-80) cc_final: 0.8126 (m-80) REVERT: B 751 GLU cc_start: 0.7832 (tt0) cc_final: 0.7621 (tt0) REVERT: C 33 LYS cc_start: 0.8143 (mttp) cc_final: 0.7882 (mtpp) REVERT: C 46 ARG cc_start: 0.8186 (ttp-170) cc_final: 0.7945 (ttp-170) REVERT: C 116 LYS cc_start: 0.8376 (ptmm) cc_final: 0.8064 (ptmm) REVERT: C 158 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7081 (pm20) REVERT: C 171 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7836 (mt-10) REVERT: C 176 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7555 (tt) REVERT: C 177 LEU cc_start: 0.8338 (tt) cc_final: 0.8100 (tp) REVERT: C 756 MET cc_start: 0.3998 (mpm) cc_final: 0.2947 (mpm) REVERT: I 26 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6454 (tm-30) REVERT: I 36 GLU cc_start: 0.7383 (tp30) cc_final: 0.7059 (tp30) REVERT: I 40 LEU cc_start: 0.7379 (mt) cc_final: 0.7071 (mm) REVERT: I 50 MET cc_start: 0.7737 (ppp) cc_final: 0.7142 (ppp) REVERT: I 74 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7193 (mm-30) REVERT: I 81 GLU cc_start: 0.7544 (mp0) cc_final: 0.7317 (mp0) REVERT: I 100 MET cc_start: 0.6933 (mmp) cc_final: 0.6628 (mmp) REVERT: I 106 LEU cc_start: 0.7700 (mp) cc_final: 0.7278 (tp) REVERT: J 65 TRP cc_start: 0.6541 (t60) cc_final: 0.6174 (t60) outliers start: 113 outliers final: 36 residues processed: 697 average time/residue: 0.7437 time to fit residues: 580.2645 Evaluate side-chains 696 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 636 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 570 THR Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 148 GLU Chi-restraints excluded: chain F residue 171 MET Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 267 GLU Chi-restraints excluded: chain F residue 305 ASP Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 409 MET Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 442 GLN Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain F residue 571 ARG Chi-restraints excluded: chain F residue 618 GLU Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 654 GLN Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 504 ASN Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 105 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 268 optimal weight: 0.5980 chunk 288 optimal weight: 0.6980 chunk 191 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 9 optimal weight: 0.0020 chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 176 optimal weight: 0.4980 chunk 150 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 ASN F 328 ASN F 603 ASN G 102 ASN A 92 ASN A 136 ASN B 504 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.124444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.101626 restraints weight = 37622.158| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.09 r_work: 0.3121 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25504 Z= 0.136 Angle : 0.572 9.148 34404 Z= 0.301 Chirality : 0.040 0.197 3769 Planarity : 0.004 0.050 4428 Dihedral : 4.558 50.669 3388 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.78 % Favored : 94.09 % Rotamer: Outliers : 4.22 % Allowed : 21.40 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.15), residues: 3077 helix: 1.48 (0.14), residues: 1519 sheet: 0.37 (0.33), residues: 242 loop : -2.26 (0.15), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 170 TYR 0.016 0.001 TYR F 30 PHE 0.025 0.001 PHE B 512 TRP 0.011 0.001 TRP F 437 HIS 0.003 0.001 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00302 (25504) covalent geometry : angle 0.57230 (34404) hydrogen bonds : bond 0.05766 ( 1146) hydrogen bonds : angle 3.99266 ( 3258) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 641 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: E 229 PHE cc_start: 0.6108 (m-80) cc_final: 0.4492 (t80) REVERT: E 262 LYS cc_start: 0.8655 (ttmm) cc_final: 0.8420 (ttpp) REVERT: E 347 ASP cc_start: 0.7971 (t70) cc_final: 0.7687 (t0) REVERT: E 430 GLU cc_start: 0.7700 (pm20) cc_final: 0.7460 (pm20) REVERT: E 512 ARG cc_start: 0.8260 (mtp85) cc_final: 0.8007 (mtp85) REVERT: E 544 GLU cc_start: 0.8114 (tt0) cc_final: 0.7847 (tt0) REVERT: E 691 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8033 (mt-10) REVERT: F 78 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8124 (mm-30) REVERT: F 104 GLU cc_start: 0.7519 (mp0) cc_final: 0.7059 (mp0) REVERT: F 108 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8613 (mp) REVERT: F 148 GLU cc_start: 0.7695 (pp20) cc_final: 0.7297 (pp20) REVERT: F 158 ASN cc_start: 0.7982 (t0) cc_final: 0.7728 (t0) REVERT: F 260 ARG cc_start: 0.8243 (mtp-110) cc_final: 0.7922 (mtp85) REVERT: F 398 ASP cc_start: 0.8051 (p0) cc_final: 0.7718 (p0) REVERT: F 411 MET cc_start: 0.4299 (tmt) cc_final: 0.4046 (tmm) REVERT: F 442 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8170 (tt0) REVERT: F 475 ILE cc_start: 0.8205 (pt) cc_final: 0.7815 (mt) REVERT: F 571 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7203 (ttp80) REVERT: F 614 GLU cc_start: 0.7966 (pp20) cc_final: 0.7686 (pp20) REVERT: G 102 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.8210 (p0) REVERT: A 6 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7438 (mpt90) REVERT: A 7 GLN cc_start: 0.8068 (pp30) cc_final: 0.7833 (pp30) REVERT: A 18 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: A 34 LYS cc_start: 0.7531 (mtpp) cc_final: 0.7138 (mttm) REVERT: A 65 LEU cc_start: 0.6622 (OUTLIER) cc_final: 0.6319 (mm) REVERT: A 95 CYS cc_start: 0.7105 (p) cc_final: 0.6796 (t) REVERT: A 114 GLU cc_start: 0.8245 (tp30) cc_final: 0.7700 (tp30) REVERT: A 122 VAL cc_start: 0.9001 (OUTLIER) cc_final: 0.8677 (t) REVERT: A 129 ILE cc_start: 0.8613 (mm) cc_final: 0.8175 (mm) REVERT: A 133 GLU cc_start: 0.7740 (mp0) cc_final: 0.7519 (mp0) REVERT: A 148 PHE cc_start: 0.8867 (m-10) cc_final: 0.8642 (m-80) REVERT: A 181 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7608 (tm-30) REVERT: A 199 GLU cc_start: 0.7870 (pm20) cc_final: 0.7595 (pm20) REVERT: A 327 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6848 (pm20) REVERT: A 380 ASP cc_start: 0.7770 (t70) cc_final: 0.7381 (t70) REVERT: A 385 ARG cc_start: 0.8292 (ttp-110) cc_final: 0.8045 (ttm-80) REVERT: A 469 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8653 (tt) REVERT: A 548 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.8083 (ttm) REVERT: A 691 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7884 (mt-10) REVERT: A 693 CYS cc_start: 0.7457 (t) cc_final: 0.7130 (t) REVERT: B 96 GLU cc_start: 0.8399 (tp30) cc_final: 0.8054 (tp30) REVERT: B 177 GLU cc_start: 0.7767 (tp30) cc_final: 0.7560 (tp30) REVERT: B 178 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7483 (mt-10) REVERT: B 212 VAL cc_start: 0.8304 (t) cc_final: 0.8018 (m) REVERT: B 260 ARG cc_start: 0.8640 (ttt90) cc_final: 0.8388 (ttt90) REVERT: B 267 GLU cc_start: 0.7708 (pm20) cc_final: 0.7469 (pm20) REVERT: B 307 THR cc_start: 0.8579 (t) cc_final: 0.8364 (t) REVERT: B 319 LEU cc_start: 0.8375 (tp) cc_final: 0.8140 (tt) REVERT: B 371 GLU cc_start: 0.7748 (tp30) cc_final: 0.7502 (tp30) REVERT: B 379 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8009 (tmmm) REVERT: B 481 LYS cc_start: 0.8523 (mtmm) cc_final: 0.8231 (mtmm) REVERT: B 504 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.8174 (p0) REVERT: B 667 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8556 (mt) REVERT: B 687 GLN cc_start: 0.7790 (mp10) cc_final: 0.7571 (mp10) REVERT: B 694 ASN cc_start: 0.8373 (m110) cc_final: 0.8140 (m110) REVERT: B 699 PHE cc_start: 0.8475 (m-80) cc_final: 0.8127 (m-80) REVERT: B 751 GLU cc_start: 0.7878 (tt0) cc_final: 0.7669 (tt0) REVERT: C 33 LYS cc_start: 0.8188 (mttp) cc_final: 0.7935 (mtpp) REVERT: C 46 ARG cc_start: 0.8202 (ttp-170) cc_final: 0.7942 (ttp-170) REVERT: C 116 LYS cc_start: 0.8485 (ptmm) cc_final: 0.8193 (ptmm) REVERT: C 158 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7132 (pm20) REVERT: C 171 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7895 (mt-10) REVERT: C 176 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7647 (tt) REVERT: C 177 LEU cc_start: 0.8311 (tt) cc_final: 0.8091 (tp) REVERT: C 756 MET cc_start: 0.4055 (mpm) cc_final: 0.2706 (mpm) REVERT: I 40 LEU cc_start: 0.7408 (mt) cc_final: 0.7161 (mm) REVERT: I 50 MET cc_start: 0.7741 (ppp) cc_final: 0.7062 (ppp) REVERT: I 74 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7651 (mm-30) REVERT: I 106 LEU cc_start: 0.7778 (mp) cc_final: 0.7369 (tp) REVERT: J 65 TRP cc_start: 0.6630 (t60) cc_final: 0.6234 (t60) outliers start: 116 outliers final: 59 residues processed: 684 average time/residue: 0.8631 time to fit residues: 660.0876 Evaluate side-chains 713 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 634 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain E residue 570 THR Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 628 VAL Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 171 MET Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 267 GLU Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 442 GLN Chi-restraints excluded: chain F residue 571 ARG Chi-restraints excluded: chain F residue 618 GLU Chi-restraints excluded: chain F residue 662 THR Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 312 ARG Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 504 ASN Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 105 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 0 optimal weight: 2.9990 chunk 266 optimal weight: 0.8980 chunk 230 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 303 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 277 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 58 ASN ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 276 ASN F 328 ASN F 603 ASN G 102 ASN A 92 ASN A 128 HIS A 136 ASN A 180 GLN A 383 ASN I 20 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.117911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.095320 restraints weight = 37675.416| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.08 r_work: 0.3026 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 25504 Z= 0.244 Angle : 0.690 10.150 34404 Z= 0.365 Chirality : 0.046 0.220 3769 Planarity : 0.005 0.055 4428 Dihedral : 4.844 45.159 3385 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.56 % Favored : 93.27 % Rotamer: Outliers : 5.31 % Allowed : 20.75 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.15), residues: 3077 helix: 1.19 (0.14), residues: 1532 sheet: 0.49 (0.34), residues: 234 loop : -2.42 (0.15), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 215 TYR 0.018 0.002 TYR B 467 PHE 0.032 0.002 PHE B 512 TRP 0.018 0.002 TRP F 55 HIS 0.007 0.001 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00587 (25504) covalent geometry : angle 0.68995 (34404) hydrogen bonds : bond 0.08756 ( 1146) hydrogen bonds : angle 4.30137 ( 3258) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 661 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 347 ASP cc_start: 0.8274 (t70) cc_final: 0.8064 (t70) REVERT: E 351 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7448 (mt-10) REVERT: E 430 GLU cc_start: 0.7676 (pm20) cc_final: 0.7433 (pm20) REVERT: E 512 ARG cc_start: 0.8283 (mtp85) cc_final: 0.8048 (mtp85) REVERT: E 544 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: E 594 SER cc_start: 0.8661 (t) cc_final: 0.8418 (m) REVERT: E 673 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.7748 (mtt-85) REVERT: E 691 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: F 78 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8032 (mm-30) REVERT: F 104 GLU cc_start: 0.7637 (mp0) cc_final: 0.7177 (mp0) REVERT: F 260 ARG cc_start: 0.8513 (mtp-110) cc_final: 0.8232 (mtp-110) REVERT: F 396 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8329 (tt) REVERT: F 398 ASP cc_start: 0.8168 (p0) cc_final: 0.7776 (p0) REVERT: F 475 ILE cc_start: 0.8285 (pt) cc_final: 0.7857 (mt) REVERT: F 571 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7481 (ttp80) REVERT: F 614 GLU cc_start: 0.8026 (pp20) cc_final: 0.7703 (pp20) REVERT: A 6 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.7509 (mpt90) REVERT: A 8 CYS cc_start: 0.8552 (t) cc_final: 0.8273 (t) REVERT: A 18 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: A 34 LYS cc_start: 0.7767 (mtpp) cc_final: 0.7390 (mttm) REVERT: A 65 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6505 (mm) REVERT: A 95 CYS cc_start: 0.7152 (p) cc_final: 0.6804 (t) REVERT: A 101 GLU cc_start: 0.7448 (mp0) cc_final: 0.7079 (mp0) REVERT: A 114 GLU cc_start: 0.8257 (tp30) cc_final: 0.7706 (tp30) REVERT: A 148 PHE cc_start: 0.8896 (m-10) cc_final: 0.8649 (m-80) REVERT: A 199 GLU cc_start: 0.7896 (pm20) cc_final: 0.7597 (pm20) REVERT: A 327 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6945 (pm20) REVERT: A 380 ASP cc_start: 0.7774 (t70) cc_final: 0.7365 (t70) REVERT: A 385 ARG cc_start: 0.8281 (ttp-110) cc_final: 0.8041 (ttm-80) REVERT: A 469 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8786 (tt) REVERT: A 508 ARG cc_start: 0.7963 (mtt-85) cc_final: 0.7733 (mtt-85) REVERT: A 636 VAL cc_start: 0.8002 (OUTLIER) cc_final: 0.7789 (t) REVERT: A 691 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: B 96 GLU cc_start: 0.8431 (tp30) cc_final: 0.8101 (tp30) REVERT: B 121 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7696 (tpp-160) REVERT: B 178 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7434 (mt-10) REVERT: B 212 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8181 (m) REVERT: B 267 GLU cc_start: 0.7799 (pm20) cc_final: 0.7557 (pm20) REVERT: B 362 MET cc_start: 0.8401 (mpm) cc_final: 0.8107 (mpt) REVERT: B 371 GLU cc_start: 0.7742 (tp30) cc_final: 0.7466 (tp30) REVERT: B 379 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8078 (tmmm) REVERT: B 481 LYS cc_start: 0.8646 (mtmm) cc_final: 0.8409 (mtmm) REVERT: B 667 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8579 (mt) REVERT: B 687 GLN cc_start: 0.7897 (mp10) cc_final: 0.7655 (mp10) REVERT: B 699 PHE cc_start: 0.8525 (m-80) cc_final: 0.8251 (m-80) REVERT: B 751 GLU cc_start: 0.7948 (tt0) cc_final: 0.7737 (tt0) REVERT: C 22 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8111 (mttt) REVERT: C 46 ARG cc_start: 0.8272 (ttp-170) cc_final: 0.8018 (ttp-170) REVERT: C 69 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8142 (tt0) REVERT: C 116 LYS cc_start: 0.8713 (ptmm) cc_final: 0.8426 (ptmm) REVERT: C 158 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7230 (pm20) REVERT: C 171 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7992 (mt-10) REVERT: C 176 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7804 (tt) REVERT: C 177 LEU cc_start: 0.8448 (tt) cc_final: 0.8171 (tp) REVERT: C 187 LYS cc_start: 0.8120 (ttpp) cc_final: 0.7829 (ttpp) REVERT: C 756 MET cc_start: 0.4283 (mpm) cc_final: 0.3191 (mpm) REVERT: I 36 GLU cc_start: 0.7368 (tp30) cc_final: 0.6710 (tp30) REVERT: I 40 LEU cc_start: 0.7502 (mt) cc_final: 0.6988 (mm) REVERT: I 50 MET cc_start: 0.7856 (ppp) cc_final: 0.7124 (ppp) REVERT: I 68 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6411 (mp10) REVERT: I 74 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7668 (mm-30) outliers start: 146 outliers final: 70 residues processed: 721 average time/residue: 0.7616 time to fit residues: 614.4498 Evaluate side-chains 754 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 661 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 544 GLU Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 628 VAL Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 673 ARG Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 267 GLU Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 396 LEU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 429 LYS Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 534 MET Chi-restraints excluded: chain F residue 571 ARG Chi-restraints excluded: chain F residue 618 GLU Chi-restraints excluded: chain F residue 662 THR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 504 ASN Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 721 LYS Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 84 optimal weight: 0.9980 chunk 178 optimal weight: 0.8980 chunk 302 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 301 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 100 optimal weight: 0.0770 chunk 43 optimal weight: 0.9980 chunk 162 optimal weight: 0.5980 chunk 285 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN F 328 ASN F 603 ASN A 92 ASN A 136 ASN A 180 GLN A 346 GLN B 694 ASN C 170 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.119466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.096785 restraints weight = 37686.888| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.11 r_work: 0.3060 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25504 Z= 0.177 Angle : 0.631 10.694 34404 Z= 0.332 Chirality : 0.043 0.210 3769 Planarity : 0.005 0.055 4428 Dihedral : 4.701 41.110 3385 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.82 % Favored : 94.02 % Rotamer: Outliers : 4.83 % Allowed : 22.17 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.15), residues: 3077 helix: 1.28 (0.14), residues: 1532 sheet: 0.48 (0.34), residues: 228 loop : -2.44 (0.15), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 486 TYR 0.017 0.001 TYR F 30 PHE 0.028 0.002 PHE F 103 TRP 0.024 0.002 TRP F 55 HIS 0.004 0.001 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00415 (25504) covalent geometry : angle 0.63059 (34404) hydrogen bonds : bond 0.07135 ( 1146) hydrogen bonds : angle 4.15668 ( 3258) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 663 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 321 TYR cc_start: 0.8833 (p90) cc_final: 0.8479 (p90) REVERT: E 347 ASP cc_start: 0.8177 (t70) cc_final: 0.7973 (t70) REVERT: E 351 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7410 (mt-10) REVERT: E 512 ARG cc_start: 0.8334 (mtp85) cc_final: 0.8066 (mtp85) REVERT: E 544 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: E 594 SER cc_start: 0.8666 (t) cc_final: 0.8411 (m) REVERT: E 691 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: F 76 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.7098 (p0) REVERT: F 78 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7969 (mm-30) REVERT: F 104 GLU cc_start: 0.7600 (mp0) cc_final: 0.7189 (mp0) REVERT: F 132 THR cc_start: 0.8886 (m) cc_final: 0.8434 (p) REVERT: F 179 MET cc_start: 0.4978 (OUTLIER) cc_final: 0.4403 (ptm) REVERT: F 398 ASP cc_start: 0.8208 (p0) cc_final: 0.7825 (p0) REVERT: F 442 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: F 457 GLU cc_start: 0.7974 (mp0) cc_final: 0.7633 (mp0) REVERT: F 475 ILE cc_start: 0.8234 (pt) cc_final: 0.7791 (mt) REVERT: F 571 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7394 (ttp80) REVERT: F 614 GLU cc_start: 0.8022 (pp20) cc_final: 0.7722 (pp20) REVERT: A 6 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.7498 (mpt90) REVERT: A 8 CYS cc_start: 0.8535 (t) cc_final: 0.8218 (t) REVERT: A 18 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: A 34 LYS cc_start: 0.7659 (mtpp) cc_final: 0.7269 (mttm) REVERT: A 65 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6621 (mm) REVERT: A 82 ARG cc_start: 0.7063 (mtt-85) cc_final: 0.6772 (mtt-85) REVERT: A 95 CYS cc_start: 0.7099 (p) cc_final: 0.6848 (t) REVERT: A 101 GLU cc_start: 0.7397 (mp0) cc_final: 0.6917 (mp0) REVERT: A 114 GLU cc_start: 0.8224 (tp30) cc_final: 0.7662 (tp30) REVERT: A 133 GLU cc_start: 0.7810 (mp0) cc_final: 0.7545 (mm-30) REVERT: A 148 PHE cc_start: 0.8923 (m-10) cc_final: 0.8704 (m-80) REVERT: A 181 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7615 (tp30) REVERT: A 199 GLU cc_start: 0.7918 (pm20) cc_final: 0.7581 (pm20) REVERT: A 272 ASP cc_start: 0.8196 (p0) cc_final: 0.7876 (p0) REVERT: A 327 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6962 (pm20) REVERT: A 374 MET cc_start: 0.7189 (mpp) cc_final: 0.6898 (mpp) REVERT: A 385 ARG cc_start: 0.8326 (ttp-110) cc_final: 0.8093 (ttm-80) REVERT: A 469 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8744 (tt) REVERT: A 508 ARG cc_start: 0.7943 (mtt-85) cc_final: 0.7709 (mtt-85) REVERT: A 549 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8441 (mm) REVERT: A 691 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7944 (mt-10) REVERT: A 712 THR cc_start: 0.8635 (t) cc_final: 0.8356 (m) REVERT: B 96 GLU cc_start: 0.8408 (tp30) cc_final: 0.8078 (tp30) REVERT: B 121 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7671 (tpp-160) REVERT: B 178 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: B 212 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.8174 (m) REVERT: B 267 GLU cc_start: 0.7751 (pm20) cc_final: 0.7521 (pm20) REVERT: B 290 MET cc_start: 0.7567 (tpt) cc_final: 0.7319 (mmp) REVERT: B 362 MET cc_start: 0.8393 (mpm) cc_final: 0.8100 (mpt) REVERT: B 371 GLU cc_start: 0.7736 (tp30) cc_final: 0.7449 (tp30) REVERT: B 481 LYS cc_start: 0.8592 (mtmm) cc_final: 0.8231 (mtmm) REVERT: B 667 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8606 (mt) REVERT: B 699 PHE cc_start: 0.8497 (m-80) cc_final: 0.8202 (m-80) REVERT: B 709 VAL cc_start: 0.8835 (t) cc_final: 0.8604 (m) REVERT: B 751 GLU cc_start: 0.7929 (tt0) cc_final: 0.7722 (tt0) REVERT: C 22 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8061 (mttt) REVERT: C 46 ARG cc_start: 0.8266 (ttp-170) cc_final: 0.8017 (ttp-170) REVERT: C 116 LYS cc_start: 0.8696 (ptmm) cc_final: 0.8391 (ptmm) REVERT: C 158 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7185 (pm20) REVERT: C 171 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: C 176 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7765 (tt) REVERT: C 177 LEU cc_start: 0.8410 (tt) cc_final: 0.8138 (tp) REVERT: C 187 LYS cc_start: 0.8128 (ttpp) cc_final: 0.7828 (ttpp) REVERT: C 188 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7365 (mt-10) REVERT: C 220 VAL cc_start: 0.8152 (m) cc_final: 0.7917 (t) REVERT: C 736 LYS cc_start: 0.8451 (tppp) cc_final: 0.8235 (tptm) REVERT: C 756 MET cc_start: 0.4267 (mpm) cc_final: 0.3155 (mpm) REVERT: I 40 LEU cc_start: 0.7518 (mt) cc_final: 0.7288 (mm) REVERT: I 50 MET cc_start: 0.7993 (ppp) cc_final: 0.7282 (ppp) REVERT: I 74 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7629 (mm-30) REVERT: I 81 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: I 106 LEU cc_start: 0.7828 (mp) cc_final: 0.7426 (tp) REVERT: I 113 ILE cc_start: 0.8640 (mt) cc_final: 0.8340 (mp) outliers start: 133 outliers final: 67 residues processed: 712 average time/residue: 0.7516 time to fit residues: 602.2312 Evaluate side-chains 748 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 658 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 424 GLU Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain E residue 544 GLU Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 628 VAL Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 55 TRP Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 148 GLU Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 267 GLU Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 429 LYS Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 442 GLN Chi-restraints excluded: chain F residue 534 MET Chi-restraints excluded: chain F residue 571 ARG Chi-restraints excluded: chain F residue 592 SER Chi-restraints excluded: chain F residue 618 GLU Chi-restraints excluded: chain F residue 662 THR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain J residue 29 ASN Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 105 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 147 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 143 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 218 optimal weight: 0.5980 chunk 216 optimal weight: 0.8980 chunk 281 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 9 optimal weight: 0.0870 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 ASN F 603 ASN A 92 ASN A 136 ASN A 481 GLN B 569 GLN C 170 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.121769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.099281 restraints weight = 37564.232| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.07 r_work: 0.3080 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25504 Z= 0.150 Angle : 0.612 11.064 34404 Z= 0.320 Chirality : 0.041 0.210 3769 Planarity : 0.005 0.054 4428 Dihedral : 4.580 39.543 3385 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.08 % Favored : 93.76 % Rotamer: Outliers : 4.25 % Allowed : 23.44 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.15), residues: 3077 helix: 1.42 (0.14), residues: 1515 sheet: 0.25 (0.33), residues: 240 loop : -2.36 (0.15), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 486 TYR 0.016 0.001 TYR F 30 PHE 0.027 0.001 PHE I 116 TRP 0.036 0.002 TRP J 65 HIS 0.004 0.001 HIS F 47 Details of bonding type rmsd covalent geometry : bond 0.00342 (25504) covalent geometry : angle 0.61189 (34404) hydrogen bonds : bond 0.06443 ( 1146) hydrogen bonds : angle 4.06644 ( 3258) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 653 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 321 TYR cc_start: 0.8813 (p90) cc_final: 0.8460 (p90) REVERT: E 347 ASP cc_start: 0.8138 (t70) cc_final: 0.7935 (t70) REVERT: E 351 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7362 (mt-10) REVERT: E 430 GLU cc_start: 0.7727 (pm20) cc_final: 0.7483 (pm20) REVERT: E 512 ARG cc_start: 0.8265 (mtp85) cc_final: 0.8023 (mtp85) REVERT: E 544 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7834 (tt0) REVERT: E 594 SER cc_start: 0.8668 (t) cc_final: 0.8409 (m) REVERT: E 691 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: F 78 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7950 (mm-30) REVERT: F 104 GLU cc_start: 0.7615 (mp0) cc_final: 0.7204 (mp0) REVERT: F 117 THR cc_start: 0.8469 (t) cc_final: 0.8139 (m) REVERT: F 132 THR cc_start: 0.8863 (m) cc_final: 0.8432 (p) REVERT: F 376 ILE cc_start: 0.7974 (mm) cc_final: 0.7548 (mp) REVERT: F 398 ASP cc_start: 0.8211 (p0) cc_final: 0.7844 (p0) REVERT: F 442 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: F 475 ILE cc_start: 0.8213 (pt) cc_final: 0.7778 (mt) REVERT: F 571 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7353 (ttp80) REVERT: F 614 GLU cc_start: 0.8098 (pp20) cc_final: 0.7815 (pp20) REVERT: A 18 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: A 34 LYS cc_start: 0.7549 (mtpp) cc_final: 0.7172 (mttm) REVERT: A 95 CYS cc_start: 0.7141 (p) cc_final: 0.6931 (t) REVERT: A 101 GLU cc_start: 0.7440 (mp0) cc_final: 0.7070 (mp0) REVERT: A 114 GLU cc_start: 0.8183 (tp30) cc_final: 0.7555 (tp30) REVERT: A 117 PHE cc_start: 0.7549 (m-10) cc_final: 0.7015 (m-80) REVERT: A 126 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7120 (pp20) REVERT: A 133 GLU cc_start: 0.7825 (mp0) cc_final: 0.7525 (mm-30) REVERT: A 148 PHE cc_start: 0.8955 (m-80) cc_final: 0.8733 (m-80) REVERT: A 181 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7580 (tp30) REVERT: A 199 GLU cc_start: 0.7913 (pm20) cc_final: 0.7607 (pm20) REVERT: A 272 ASP cc_start: 0.8209 (p0) cc_final: 0.7875 (p0) REVERT: A 327 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6924 (pm20) REVERT: A 374 MET cc_start: 0.7202 (mpp) cc_final: 0.6925 (mpp) REVERT: A 469 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8695 (tt) REVERT: A 508 ARG cc_start: 0.7921 (mtt-85) cc_final: 0.7673 (mtt-85) REVERT: A 548 MET cc_start: 0.8356 (ttp) cc_final: 0.8086 (ttm) REVERT: A 549 LEU cc_start: 0.8716 (mp) cc_final: 0.8478 (mm) REVERT: A 691 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7940 (mt-10) REVERT: B 90 GLU cc_start: 0.8353 (tt0) cc_final: 0.8150 (tt0) REVERT: B 96 GLU cc_start: 0.8405 (tp30) cc_final: 0.8084 (tp30) REVERT: B 121 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7657 (tpp-160) REVERT: B 178 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: B 212 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.8188 (m) REVERT: B 260 ARG cc_start: 0.8630 (ttt90) cc_final: 0.8377 (ttt90) REVERT: B 267 GLU cc_start: 0.7719 (pm20) cc_final: 0.7504 (pm20) REVERT: B 290 MET cc_start: 0.7408 (tpt) cc_final: 0.7176 (mmp) REVERT: B 362 MET cc_start: 0.8403 (mpm) cc_final: 0.8124 (mpt) REVERT: B 371 GLU cc_start: 0.7753 (tp30) cc_final: 0.7467 (tp30) REVERT: B 481 LYS cc_start: 0.8582 (mtmm) cc_final: 0.8234 (mtmm) REVERT: B 667 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8588 (mt) REVERT: B 699 PHE cc_start: 0.8509 (m-80) cc_final: 0.8179 (m-80) REVERT: B 709 VAL cc_start: 0.8874 (t) cc_final: 0.8617 (m) REVERT: B 751 GLU cc_start: 0.7905 (tt0) cc_final: 0.7686 (tt0) REVERT: C 22 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8084 (mttt) REVERT: C 46 ARG cc_start: 0.8251 (ttp-170) cc_final: 0.8007 (ttp-170) REVERT: C 116 LYS cc_start: 0.8699 (ptmm) cc_final: 0.8410 (ptmm) REVERT: C 158 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7227 (pm20) REVERT: C 176 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7691 (tt) REVERT: C 177 LEU cc_start: 0.8419 (tt) cc_final: 0.8130 (tp) REVERT: C 187 LYS cc_start: 0.8180 (ttpp) cc_final: 0.7878 (ttpp) REVERT: C 188 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7366 (mt-10) REVERT: C 756 MET cc_start: 0.4161 (mpm) cc_final: 0.3143 (mpm) REVERT: I 40 LEU cc_start: 0.7536 (mt) cc_final: 0.7320 (mm) REVERT: I 50 MET cc_start: 0.8184 (ppp) cc_final: 0.7820 (ppp) REVERT: I 68 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6403 (mp10) REVERT: I 74 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7627 (mm-30) REVERT: I 82 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7932 (tm-30) REVERT: I 103 LEU cc_start: 0.7466 (mm) cc_final: 0.7196 (tp) REVERT: I 106 LEU cc_start: 0.7826 (mp) cc_final: 0.7405 (tp) REVERT: I 113 ILE cc_start: 0.8622 (mt) cc_final: 0.8322 (mp) REVERT: J 65 TRP cc_start: 0.6852 (t60) cc_final: 0.6501 (t60) outliers start: 117 outliers final: 68 residues processed: 700 average time/residue: 0.7351 time to fit residues: 575.4759 Evaluate side-chains 743 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 657 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain E residue 544 GLU Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 613 GLU Chi-restraints excluded: chain E residue 628 VAL Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 55 TRP Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 267 GLU Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 343 MET Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 429 LYS Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 442 GLN Chi-restraints excluded: chain F residue 534 MET Chi-restraints excluded: chain F residue 571 ARG Chi-restraints excluded: chain F residue 592 SER Chi-restraints excluded: chain F residue 618 GLU Chi-restraints excluded: chain F residue 662 THR Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain J residue 29 ASN Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 109 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 160 optimal weight: 0.9980 chunk 230 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 234 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 6 optimal weight: 0.0170 chunk 65 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 171 optimal weight: 0.0010 chunk 135 optimal weight: 3.9990 overall best weight: 0.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN A 136 ASN B 687 GLN C 170 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.122799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.100307 restraints weight = 37685.896| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.07 r_work: 0.3099 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25504 Z= 0.135 Angle : 0.607 11.640 34404 Z= 0.315 Chirality : 0.041 0.210 3769 Planarity : 0.005 0.052 4428 Dihedral : 4.498 39.094 3385 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.59 % Favored : 94.28 % Rotamer: Outliers : 3.74 % Allowed : 24.24 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.15), residues: 3077 helix: 1.52 (0.14), residues: 1523 sheet: 0.19 (0.33), residues: 247 loop : -2.35 (0.15), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 385 TYR 0.015 0.001 TYR F 30 PHE 0.027 0.001 PHE I 116 TRP 0.030 0.001 TRP J 65 HIS 0.003 0.001 HIS F 47 Details of bonding type rmsd covalent geometry : bond 0.00300 (25504) covalent geometry : angle 0.60654 (34404) hydrogen bonds : bond 0.05844 ( 1146) hydrogen bonds : angle 4.00905 ( 3258) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 660 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 321 TYR cc_start: 0.8820 (p90) cc_final: 0.8449 (p90) REVERT: E 430 GLU cc_start: 0.7713 (pm20) cc_final: 0.7473 (pm20) REVERT: E 512 ARG cc_start: 0.8265 (mtp85) cc_final: 0.7985 (mtp85) REVERT: E 544 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7803 (tt0) REVERT: E 594 SER cc_start: 0.8638 (t) cc_final: 0.8392 (m) REVERT: E 691 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: F 104 GLU cc_start: 0.7580 (mp0) cc_final: 0.7165 (mp0) REVERT: F 117 THR cc_start: 0.8366 (t) cc_final: 0.8085 (m) REVERT: F 132 THR cc_start: 0.8865 (m) cc_final: 0.8425 (p) REVERT: F 256 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7786 (mm-30) REVERT: F 288 LYS cc_start: 0.8420 (tttm) cc_final: 0.8107 (ttmm) REVERT: F 376 ILE cc_start: 0.7927 (mm) cc_final: 0.7700 (mm) REVERT: F 398 ASP cc_start: 0.8251 (p0) cc_final: 0.7877 (p0) REVERT: F 442 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: F 475 ILE cc_start: 0.8162 (pt) cc_final: 0.7743 (mt) REVERT: F 571 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7290 (ttp80) REVERT: F 614 GLU cc_start: 0.8067 (pp20) cc_final: 0.7808 (pp20) REVERT: A 6 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.7404 (mpt90) REVERT: A 18 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: A 34 LYS cc_start: 0.7545 (mtpp) cc_final: 0.7176 (mttm) REVERT: A 95 CYS cc_start: 0.7212 (p) cc_final: 0.7010 (t) REVERT: A 101 GLU cc_start: 0.7451 (mp0) cc_final: 0.6993 (mp0) REVERT: A 114 GLU cc_start: 0.8141 (tp30) cc_final: 0.7508 (tp30) REVERT: A 116 ARG cc_start: 0.7885 (ptt180) cc_final: 0.7664 (ptp90) REVERT: A 117 PHE cc_start: 0.7618 (m-10) cc_final: 0.6924 (m-80) REVERT: A 122 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8613 (t) REVERT: A 133 GLU cc_start: 0.7822 (mp0) cc_final: 0.7453 (mm-30) REVERT: A 148 PHE cc_start: 0.8965 (m-80) cc_final: 0.8710 (m-80) REVERT: A 181 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7562 (tp30) REVERT: A 199 GLU cc_start: 0.7892 (pm20) cc_final: 0.7586 (pm20) REVERT: A 272 ASP cc_start: 0.8149 (p0) cc_final: 0.7832 (p0) REVERT: A 327 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6815 (pm20) REVERT: A 372 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7033 (mm-30) REVERT: A 374 MET cc_start: 0.7242 (mpp) cc_final: 0.6944 (mpp) REVERT: A 469 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8675 (tt) REVERT: A 508 ARG cc_start: 0.7904 (mtt-85) cc_final: 0.7678 (mtt-85) REVERT: A 548 MET cc_start: 0.8343 (ttp) cc_final: 0.8080 (ttm) REVERT: A 549 LEU cc_start: 0.8701 (mp) cc_final: 0.8450 (mm) REVERT: A 691 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7880 (mt-10) REVERT: B 96 GLU cc_start: 0.8401 (tp30) cc_final: 0.8082 (tp30) REVERT: B 178 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7496 (mt-10) REVERT: B 212 VAL cc_start: 0.8424 (OUTLIER) cc_final: 0.8141 (m) REVERT: B 267 GLU cc_start: 0.7709 (pm20) cc_final: 0.7484 (pm20) REVERT: B 362 MET cc_start: 0.8366 (mpm) cc_final: 0.8055 (mpt) REVERT: B 371 GLU cc_start: 0.7746 (tp30) cc_final: 0.7465 (tp30) REVERT: B 379 LYS cc_start: 0.8367 (pttm) cc_final: 0.8140 (tmmm) REVERT: B 481 LYS cc_start: 0.8572 (mtmm) cc_final: 0.8232 (mtmm) REVERT: B 667 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8579 (mt) REVERT: B 699 PHE cc_start: 0.8448 (m-80) cc_final: 0.8163 (m-80) REVERT: B 709 VAL cc_start: 0.8822 (t) cc_final: 0.8605 (m) REVERT: B 751 GLU cc_start: 0.7900 (tt0) cc_final: 0.7683 (tt0) REVERT: C 2 GLU cc_start: 0.7644 (mp0) cc_final: 0.7396 (mp0) REVERT: C 22 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.8073 (mttt) REVERT: C 46 ARG cc_start: 0.8253 (ttp-170) cc_final: 0.8007 (ttp-170) REVERT: C 69 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: C 116 LYS cc_start: 0.8667 (ptmm) cc_final: 0.8361 (ptmm) REVERT: C 158 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7211 (pm20) REVERT: C 176 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7666 (tt) REVERT: C 177 LEU cc_start: 0.8419 (tt) cc_final: 0.8136 (tp) REVERT: C 187 LYS cc_start: 0.8143 (ttpp) cc_final: 0.7831 (ttpp) REVERT: C 188 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7340 (mt-10) REVERT: C 756 MET cc_start: 0.4161 (mpm) cc_final: 0.3228 (mpm) REVERT: I 40 LEU cc_start: 0.7553 (mt) cc_final: 0.7336 (mm) REVERT: I 50 MET cc_start: 0.8102 (ppp) cc_final: 0.7781 (ppp) REVERT: I 68 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6453 (mp10) REVERT: I 74 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7571 (mm-30) REVERT: I 81 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: I 82 GLU cc_start: 0.8292 (tm-30) cc_final: 0.8091 (tm-30) REVERT: I 103 LEU cc_start: 0.7451 (mm) cc_final: 0.7150 (tp) REVERT: I 106 LEU cc_start: 0.7824 (mp) cc_final: 0.7394 (tp) REVERT: I 113 ILE cc_start: 0.8633 (mt) cc_final: 0.8335 (mp) outliers start: 103 outliers final: 64 residues processed: 700 average time/residue: 0.7662 time to fit residues: 600.7056 Evaluate side-chains 738 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 654 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain E residue 544 GLU Chi-restraints excluded: chain E residue 597 GLU Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 628 VAL Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 55 TRP Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 267 GLU Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 429 LYS Chi-restraints excluded: chain F residue 442 GLN Chi-restraints excluded: chain F residue 571 ARG Chi-restraints excluded: chain F residue 592 SER Chi-restraints excluded: chain F residue 618 GLU Chi-restraints excluded: chain F residue 662 THR Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain J residue 29 ASN Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 88 LYS Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 272 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 285 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 129 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 266 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN A 136 ASN A 481 GLN C 170 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.120677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.098209 restraints weight = 37619.195| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.06 r_work: 0.3060 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25504 Z= 0.176 Angle : 0.653 12.303 34404 Z= 0.340 Chirality : 0.043 0.220 3769 Planarity : 0.005 0.056 4428 Dihedral : 4.632 39.226 3385 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.21 % Favored : 93.63 % Rotamer: Outliers : 3.42 % Allowed : 25.00 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.15), residues: 3077 helix: 1.39 (0.14), residues: 1531 sheet: 0.41 (0.34), residues: 233 loop : -2.37 (0.15), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 385 TYR 0.017 0.002 TYR F 30 PHE 0.029 0.002 PHE I 116 TRP 0.033 0.002 TRP J 65 HIS 0.004 0.001 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00411 (25504) covalent geometry : angle 0.65306 (34404) hydrogen bonds : bond 0.07102 ( 1146) hydrogen bonds : angle 4.11973 ( 3258) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 655 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 321 TYR cc_start: 0.8822 (p90) cc_final: 0.8455 (p90) REVERT: E 430 GLU cc_start: 0.7709 (pm20) cc_final: 0.7466 (pm20) REVERT: E 512 ARG cc_start: 0.8223 (mtp85) cc_final: 0.7983 (mtp85) REVERT: E 544 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: E 594 SER cc_start: 0.8644 (t) cc_final: 0.8404 (m) REVERT: E 623 GLU cc_start: 0.7948 (tp30) cc_final: 0.7484 (tt0) REVERT: E 691 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8075 (mt-10) REVERT: F 104 GLU cc_start: 0.7586 (mp0) cc_final: 0.7169 (mp0) REVERT: F 117 THR cc_start: 0.8460 (t) cc_final: 0.8161 (m) REVERT: F 132 THR cc_start: 0.8847 (m) cc_final: 0.8413 (p) REVERT: F 179 MET cc_start: 0.5291 (OUTLIER) cc_final: 0.4744 (ptm) REVERT: F 256 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7721 (mm-30) REVERT: F 288 LYS cc_start: 0.8517 (tttm) cc_final: 0.8211 (ttmm) REVERT: F 376 ILE cc_start: 0.8039 (mm) cc_final: 0.7603 (mp) REVERT: F 398 ASP cc_start: 0.8240 (p0) cc_final: 0.7870 (p0) REVERT: F 442 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8247 (tt0) REVERT: F 475 ILE cc_start: 0.8217 (pt) cc_final: 0.7795 (mt) REVERT: F 571 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7286 (ttp80) REVERT: F 614 GLU cc_start: 0.8085 (pp20) cc_final: 0.7822 (pp20) REVERT: A 6 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.7420 (mpt90) REVERT: A 8 CYS cc_start: 0.8536 (t) cc_final: 0.8230 (t) REVERT: A 18 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: A 34 LYS cc_start: 0.7594 (mtpp) cc_final: 0.7226 (mttm) REVERT: A 50 ASP cc_start: 0.7766 (t0) cc_final: 0.7398 (t0) REVERT: A 104 LYS cc_start: 0.7162 (ttmt) cc_final: 0.6956 (ttmt) REVERT: A 113 LYS cc_start: 0.8582 (tttm) cc_final: 0.8284 (ttpp) REVERT: A 114 GLU cc_start: 0.8115 (tp30) cc_final: 0.7570 (tp30) REVERT: A 117 PHE cc_start: 0.7680 (m-10) cc_final: 0.7131 (m-80) REVERT: A 133 GLU cc_start: 0.7816 (mp0) cc_final: 0.7489 (mm-30) REVERT: A 148 PHE cc_start: 0.8984 (m-80) cc_final: 0.8729 (m-80) REVERT: A 181 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7616 (tp30) REVERT: A 199 GLU cc_start: 0.7920 (pm20) cc_final: 0.7612 (pm20) REVERT: A 272 ASP cc_start: 0.8180 (p0) cc_final: 0.7837 (p0) REVERT: A 327 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6799 (pm20) REVERT: A 372 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7079 (mm-30) REVERT: A 374 MET cc_start: 0.7242 (mpp) cc_final: 0.6986 (mpp) REVERT: A 469 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8734 (tt) REVERT: A 508 ARG cc_start: 0.7953 (mtt-85) cc_final: 0.7734 (mtt-85) REVERT: A 548 MET cc_start: 0.8356 (ttp) cc_final: 0.8105 (ttm) REVERT: A 549 LEU cc_start: 0.8722 (mp) cc_final: 0.8476 (mm) REVERT: A 691 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: B 96 GLU cc_start: 0.8405 (tp30) cc_final: 0.8088 (tp30) REVERT: B 178 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7506 (mt-10) REVERT: B 212 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8253 (m) REVERT: B 267 GLU cc_start: 0.7706 (pm20) cc_final: 0.7491 (pm20) REVERT: B 287 ARG cc_start: 0.8523 (tmm-80) cc_final: 0.8210 (ttm-80) REVERT: B 362 MET cc_start: 0.8412 (mpm) cc_final: 0.8103 (mpt) REVERT: B 371 GLU cc_start: 0.7758 (tp30) cc_final: 0.7457 (tp30) REVERT: B 379 LYS cc_start: 0.8375 (pttm) cc_final: 0.8151 (tmmm) REVERT: B 481 LYS cc_start: 0.8617 (mtmm) cc_final: 0.8260 (mtmm) REVERT: B 667 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8617 (mt) REVERT: B 699 PHE cc_start: 0.8506 (m-80) cc_final: 0.8189 (m-80) REVERT: B 709 VAL cc_start: 0.8868 (t) cc_final: 0.8633 (m) REVERT: B 751 GLU cc_start: 0.7966 (tt0) cc_final: 0.7755 (tt0) REVERT: C 2 GLU cc_start: 0.7680 (mp0) cc_final: 0.7435 (mp0) REVERT: C 22 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8095 (mttt) REVERT: C 46 ARG cc_start: 0.8236 (ttp-170) cc_final: 0.8006 (ttp-170) REVERT: C 69 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8099 (tt0) REVERT: C 116 LYS cc_start: 0.8711 (ptmm) cc_final: 0.8412 (ptmm) REVERT: C 158 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7187 (pm20) REVERT: C 176 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7805 (tt) REVERT: C 177 LEU cc_start: 0.8453 (tt) cc_final: 0.8156 (tp) REVERT: C 187 LYS cc_start: 0.8200 (ttpp) cc_final: 0.7889 (ttpp) REVERT: C 188 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7383 (mt-10) REVERT: C 756 MET cc_start: 0.4200 (mpm) cc_final: 0.3347 (mpm) REVERT: I 40 LEU cc_start: 0.7585 (mt) cc_final: 0.7373 (mm) REVERT: I 50 MET cc_start: 0.8182 (ppp) cc_final: 0.7841 (ppp) REVERT: I 68 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6469 (mp10) REVERT: I 74 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7592 (mm-30) REVERT: I 81 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: I 106 LEU cc_start: 0.7884 (mp) cc_final: 0.7447 (tp) REVERT: I 113 ILE cc_start: 0.8659 (mt) cc_final: 0.8366 (mp) outliers start: 94 outliers final: 62 residues processed: 695 average time/residue: 0.7489 time to fit residues: 582.0138 Evaluate side-chains 734 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 652 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain E residue 544 GLU Chi-restraints excluded: chain E residue 597 GLU Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 628 VAL Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain F residue 55 TRP Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 267 GLU Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 429 LYS Chi-restraints excluded: chain F residue 442 GLN Chi-restraints excluded: chain F residue 571 ARG Chi-restraints excluded: chain F residue 592 SER Chi-restraints excluded: chain F residue 662 THR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain J residue 29 ASN Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 88 LYS Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 111 optimal weight: 0.7980 chunk 155 optimal weight: 0.0770 chunk 53 optimal weight: 0.6980 chunk 72 optimal weight: 0.0170 chunk 291 optimal weight: 0.7980 chunk 188 optimal weight: 0.8980 chunk 205 optimal weight: 1.9990 chunk 290 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 259 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 136 ASN C 170 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.122201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.099754 restraints weight = 37542.641| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.06 r_work: 0.3088 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25504 Z= 0.144 Angle : 0.629 11.618 34404 Z= 0.326 Chirality : 0.041 0.212 3769 Planarity : 0.005 0.051 4428 Dihedral : 4.534 38.648 3385 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.65 % Favored : 94.18 % Rotamer: Outliers : 3.23 % Allowed : 25.25 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.15), residues: 3077 helix: 1.52 (0.14), residues: 1515 sheet: 0.18 (0.33), residues: 250 loop : -2.32 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 385 TYR 0.015 0.001 TYR F 30 PHE 0.028 0.001 PHE I 116 TRP 0.028 0.002 TRP J 65 HIS 0.003 0.001 HIS F 47 Details of bonding type rmsd covalent geometry : bond 0.00325 (25504) covalent geometry : angle 0.62863 (34404) hydrogen bonds : bond 0.06095 ( 1146) hydrogen bonds : angle 4.02993 ( 3258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12087.51 seconds wall clock time: 205 minutes 26.12 seconds (12326.12 seconds total)