Starting phenix.real_space_refine on Mon May 26 09:27:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y7m_39020/05_2025/8y7m_39020.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y7m_39020/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8y7m_39020/05_2025/8y7m_39020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y7m_39020/05_2025/8y7m_39020.map" model { file = "/net/cci-nas-00/data/ceres_data/8y7m_39020/05_2025/8y7m_39020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y7m_39020/05_2025/8y7m_39020.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 2} 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, 'GLN:plan1': 1, 'ARG:plan': 4, '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: {'GLN:plan1': 1, 'ASP:plan': 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, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 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: 15.09, per 1000 atoms: 0.60 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: 5.48 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 2.38 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: 7.82 Time building geometry restraints manager: 6.47 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: 15.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.180 Set scattering table: 0.200 Process input model: 51.210 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 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:10.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.390 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), 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 TRP 0.044 0.002 TRP B 437 HIS 0.003 0.001 HIS F 47 PHE 0.027 0.001 PHE B 512 TYR 0.016 0.001 TYR F 30 ARG 0.010 0.000 ARG C 737 Details of bonding type rmsd hydrogen bonds : bond 0.18252 ( 1146) hydrogen bonds : angle 5.40832 ( 3258) covalent geometry : bond 0.00317 (25504) covalent geometry : angle 0.63837 (34404) *********************** 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 : 2.627 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: 1.4405 time to fit residues: 1299.0276 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 : 2.638 ------------------------------------------------------------------------------- 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 259 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 240 optimal weight: 0.0870 chunk 93 optimal weight: 0.5980 chunk 146 optimal weight: 0.4980 chunk 179 optimal weight: 0.9990 chunk 278 optimal weight: 0.0570 overall best weight: 0.4476 ------------------------------------------------------------------------------- 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 499 ASN F 124 GLN F 335 ASN F 476 ASN F 549 GLN F 569 GLN F 597 ASN ** F 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 C 728 GLN I 20 GLN J 104 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.127705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105155 restraints weight = 38097.784| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.06 r_work: 0.3181 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25504 Z= 0.167 Angle : 0.660 9.165 34404 Z= 0.345 Chirality : 0.043 0.197 3769 Planarity : 0.005 0.064 4428 Dihedral : 5.082 58.100 3392 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.95 % Favored : 93.92 % Rotamer: Outliers : 3.16 % Allowed : 14.75 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 3077 helix: 1.16 (0.14), residues: 1514 sheet: 0.54 (0.35), residues: 212 loop : -2.23 (0.15), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 437 HIS 0.004 0.001 HIS A 41 PHE 0.022 0.002 PHE B 512 TYR 0.021 0.002 TYR A 48 ARG 0.010 0.001 ARG E 269 Details of bonding type rmsd hydrogen bonds : bond 0.06529 ( 1146) hydrogen bonds : angle 4.21799 ( 3258) covalent geometry : bond 0.00371 (25504) covalent geometry : angle 0.65977 (34404) *********************** 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 745 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 658 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 262 LYS cc_start: 0.8724 (ttmm) cc_final: 0.8416 (tttp) REVERT: E 347 ASP cc_start: 0.7845 (t70) cc_final: 0.7634 (t70) REVERT: E 512 ARG cc_start: 0.8301 (mtp85) cc_final: 0.7926 (mtp85) REVERT: E 673 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7827 (mtt-85) REVERT: F 8 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8007 (mp) REVERT: F 104 GLU cc_start: 0.7218 (mp0) cc_final: 0.6634 (mp0) REVERT: F 109 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7974 (mm-30) REVERT: F 130 ASP cc_start: 0.7629 (t0) cc_final: 0.7385 (t0) REVERT: F 158 ASN cc_start: 0.7940 (t0) cc_final: 0.7705 (t0) REVERT: F 317 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7165 (mpm) REVERT: F 395 LEU cc_start: 0.8131 (tt) cc_final: 0.7894 (tp) REVERT: F 398 ASP cc_start: 0.7661 (p0) cc_final: 0.7381 (p0) REVERT: F 409 MET cc_start: 0.6504 (OUTLIER) cc_final: 0.6280 (ptt) REVERT: F 475 ILE cc_start: 0.8117 (pt) cc_final: 0.7862 (mt) REVERT: F 614 GLU cc_start: 0.7839 (pp20) cc_final: 0.7584 (pp20) REVERT: G 90 MET cc_start: 0.8554 (mmp) cc_final: 0.8351 (mmt) REVERT: G 102 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8501 (p0) REVERT: A 7 GLN cc_start: 0.8006 (pp30) cc_final: 0.7507 (pp30) REVERT: A 18 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: A 19 LYS cc_start: 0.8212 (mttt) cc_final: 0.7966 (mttt) REVERT: A 38 ILE cc_start: 0.8218 (mm) cc_final: 0.7991 (mt) REVERT: A 95 CYS cc_start: 0.7101 (p) cc_final: 0.6552 (t) REVERT: A 114 GLU cc_start: 0.8184 (tp30) cc_final: 0.7804 (tp30) REVERT: A 122 VAL cc_start: 0.8965 (OUTLIER) cc_final: 0.8664 (t) REVERT: A 133 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7021 (mp0) REVERT: A 251 LYS cc_start: 0.8133 (mmtp) cc_final: 0.7801 (mmmm) REVERT: A 327 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6760 (pm20) REVERT: A 382 ASP cc_start: 0.8130 (p0) cc_final: 0.7752 (p0) REVERT: A 549 LEU cc_start: 0.8731 (mt) cc_final: 0.8375 (mm) REVERT: B 59 THR cc_start: 0.8864 (m) cc_final: 0.8641 (p) REVERT: B 264 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8121 (mt-10) REVERT: B 267 GLU cc_start: 0.7518 (pm20) cc_final: 0.7276 (pm20) REVERT: B 435 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8321 (m) REVERT: B 533 ASN cc_start: 0.8871 (OUTLIER) cc_final: 0.8490 (m-40) REVERT: B 557 TYR cc_start: 0.8342 (t80) cc_final: 0.8079 (t80) REVERT: B 751 GLU cc_start: 0.7803 (tt0) cc_final: 0.7578 (tt0) REVERT: C 46 ARG cc_start: 0.8128 (ttp-170) cc_final: 0.7830 (ttp-170) REVERT: C 756 MET cc_start: 0.4404 (mpm) cc_final: 0.4082 (mpm) REVERT: I 26 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6719 (tm-30) REVERT: I 74 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7007 (mm-30) REVERT: I 75 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7104 (mm-30) REVERT: I 106 LEU cc_start: 0.7606 (mp) cc_final: 0.7399 (tp) REVERT: J 50 MET cc_start: 0.4160 (pmm) cc_final: 0.3952 (pmm) REVERT: J 65 TRP cc_start: 0.6282 (t60) cc_final: 0.6043 (t60) outliers start: 87 outliers final: 24 residues processed: 686 average time/residue: 1.5426 time to fit residues: 1195.0595 Evaluate side-chains 659 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 623 time to evaluate : 2.627 ------------------------------------------------------------------------------- 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 344 GLU 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 8 LEU 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 317 MET Chi-restraints excluded: chain F residue 409 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 435 THR Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 667 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 31 MET 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 286 optimal weight: 0.9990 chunk 177 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 214 optimal weight: 0.9980 chunk 302 optimal weight: 0.6980 chunk 85 optimal weight: 0.3980 chunk 270 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 209 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 217 GLN E 412 ASN E 452 HIS F 284 ASN F 460 GLN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.120673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.098061 restraints weight = 37700.902| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.08 r_work: 0.3083 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 25504 Z= 0.200 Angle : 0.650 9.699 34404 Z= 0.345 Chirality : 0.044 0.237 3769 Planarity : 0.005 0.059 4428 Dihedral : 4.967 55.512 3388 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.24 % Favored : 93.60 % Rotamer: Outliers : 3.96 % Allowed : 18.68 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 3077 helix: 1.16 (0.14), residues: 1537 sheet: 0.50 (0.34), residues: 221 loop : -2.36 (0.15), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 78 HIS 0.004 0.001 HIS E 326 PHE 0.025 0.002 PHE F 166 TYR 0.019 0.002 TYR F 30 ARG 0.006 0.001 ARG A 204 Details of bonding type rmsd hydrogen bonds : bond 0.07953 ( 1146) hydrogen bonds : angle 4.23870 ( 3258) covalent geometry : bond 0.00461 (25504) covalent geometry : angle 0.65014 (34404) *********************** 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 771 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 662 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 262 LYS cc_start: 0.8815 (ttmm) cc_final: 0.8572 (ttpp) REVERT: E 347 ASP cc_start: 0.8026 (t70) cc_final: 0.7813 (t70) REVERT: E 430 GLU cc_start: 0.7588 (pm20) cc_final: 0.7350 (pm20) REVERT: E 512 ARG cc_start: 0.8312 (mtp85) cc_final: 0.7962 (mtp85) REVERT: E 544 GLU cc_start: 0.8173 (tt0) cc_final: 0.7876 (tt0) REVERT: E 604 GLU cc_start: 0.5350 (mm-30) cc_final: 0.5120 (mm-30) REVERT: E 667 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8223 (mt) REVERT: F 104 GLU cc_start: 0.7468 (mp0) cc_final: 0.7016 (mp0) REVERT: F 120 ASP cc_start: 0.7325 (p0) cc_final: 0.7107 (p0) REVERT: F 297 GLU cc_start: 0.7957 (pt0) cc_final: 0.7678 (pt0) REVERT: F 387 LYS cc_start: 0.8241 (tttp) cc_final: 0.8014 (tttp) REVERT: F 398 ASP cc_start: 0.7918 (p0) cc_final: 0.7587 (p0) REVERT: F 411 MET cc_start: 0.4551 (tmt) cc_final: 0.3978 (ppp) REVERT: F 442 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8315 (tt0) REVERT: F 475 ILE cc_start: 0.8258 (pt) cc_final: 0.7897 (mt) REVERT: F 571 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7537 (ttp80) REVERT: F 614 GLU cc_start: 0.7861 (pp20) cc_final: 0.7613 (pp20) REVERT: G 102 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.8311 (p0) REVERT: A 16 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7852 (mt) REVERT: A 18 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: A 19 LYS cc_start: 0.8448 (mttt) cc_final: 0.8131 (mttt) REVERT: A 34 LYS cc_start: 0.7708 (mtpp) cc_final: 0.7371 (mttm) REVERT: A 95 CYS cc_start: 0.7006 (p) cc_final: 0.6605 (t) REVERT: A 114 GLU cc_start: 0.8296 (tp30) cc_final: 0.7786 (tp30) REVERT: A 116 ARG cc_start: 0.7630 (ptp90) cc_final: 0.7332 (ttp80) REVERT: A 122 VAL cc_start: 0.9064 (OUTLIER) cc_final: 0.8742 (t) REVERT: A 128 HIS cc_start: 0.7451 (m-70) cc_final: 0.7038 (m-70) REVERT: A 129 ILE cc_start: 0.8724 (mm) cc_final: 0.8522 (mm) REVERT: A 133 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7467 (mp0) REVERT: A 148 PHE cc_start: 0.8792 (m-10) cc_final: 0.8310 (m-80) REVERT: A 163 LEU cc_start: 0.8113 (mt) cc_final: 0.7867 (mt) REVERT: A 170 ARG cc_start: 0.8387 (mtp180) cc_final: 0.8168 (mtm-85) REVERT: A 327 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6891 (pm20) REVERT: A 372 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.7089 (mm-30) REVERT: A 374 MET cc_start: 0.7031 (mpp) cc_final: 0.6727 (mpp) REVERT: A 386 ASP cc_start: 0.7716 (m-30) cc_final: 0.7371 (m-30) REVERT: A 469 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8727 (tt) REVERT: A 548 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8158 (ttm) REVERT: A 691 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: A 693 CYS cc_start: 0.7426 (t) cc_final: 0.7225 (t) REVERT: B 178 GLU cc_start: 0.7645 (tp30) cc_final: 0.7234 (mm-30) REVERT: B 212 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.8024 (m) REVERT: B 264 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8226 (mt-10) REVERT: B 267 GLU cc_start: 0.7778 (pm20) cc_final: 0.7541 (pm20) REVERT: B 319 LEU cc_start: 0.8368 (tp) cc_final: 0.8092 (tt) REVERT: B 371 GLU cc_start: 0.7786 (tp30) cc_final: 0.7482 (tp30) REVERT: B 386 ARG cc_start: 0.8041 (mtp-110) cc_final: 0.7455 (ttm-80) REVERT: B 403 LEU cc_start: 0.8768 (tp) cc_final: 0.8535 (tt) REVERT: B 435 THR cc_start: 0.8806 (OUTLIER) cc_final: 0.8590 (m) REVERT: B 481 LYS cc_start: 0.8534 (mtmm) cc_final: 0.8124 (mtmm) REVERT: B 557 TYR cc_start: 0.8276 (t80) cc_final: 0.8074 (t80) REVERT: B 667 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8532 (mt) REVERT: B 687 GLN cc_start: 0.7770 (mp10) cc_final: 0.7530 (mp10) REVERT: B 694 ASN cc_start: 0.8393 (m110) cc_final: 0.8161 (m110) REVERT: B 699 PHE cc_start: 0.8478 (m-80) cc_final: 0.8166 (m-80) REVERT: B 751 GLU cc_start: 0.7821 (tt0) cc_final: 0.7587 (tt0) REVERT: C 46 ARG cc_start: 0.8247 (ttp-170) cc_final: 0.7995 (ttp-170) REVERT: C 69 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8134 (tt0) REVERT: C 116 LYS cc_start: 0.8360 (ptmm) cc_final: 0.8039 (ptmm) REVERT: C 143 ARG cc_start: 0.6777 (mpp-170) cc_final: 0.6497 (mtp180) REVERT: C 171 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8015 (mt-10) REVERT: C 176 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7593 (tt) REVERT: C 177 LEU cc_start: 0.8363 (tt) cc_final: 0.8077 (tp) REVERT: C 735 MET cc_start: 0.7873 (ppp) cc_final: 0.7481 (pp-130) REVERT: C 736 LYS cc_start: 0.8514 (tppp) cc_final: 0.8222 (tppp) REVERT: C 756 MET cc_start: 0.4563 (mpm) cc_final: 0.3834 (mpm) REVERT: I 26 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6506 (tm-30) REVERT: I 74 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7278 (mm-30) REVERT: I 75 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7317 (mm-30) REVERT: I 81 GLU cc_start: 0.7523 (mp0) cc_final: 0.7296 (mp0) REVERT: I 100 MET cc_start: 0.6977 (mmp) cc_final: 0.6660 (mmp) REVERT: I 106 LEU cc_start: 0.7762 (mp) cc_final: 0.7388 (tp) REVERT: J 50 MET cc_start: 0.4377 (pmm) cc_final: 0.4158 (pmm) REVERT: J 65 TRP cc_start: 0.6584 (t60) cc_final: 0.6265 (t60) REVERT: J 100 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7996 (mmm) outliers start: 109 outliers final: 43 residues processed: 699 average time/residue: 1.6445 time to fit residues: 1288.1836 Evaluate side-chains 701 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 637 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 344 GLU Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain E residue 613 GLU Chi-restraints excluded: chain E residue 667 LEU 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 171 MET Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 218 LEU 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 442 GLN 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 102 ASN Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain A residue 16 LEU 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 327 GLU Chi-restraints excluded: chain A residue 372 GLU 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 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 212 VAL Chi-restraints excluded: chain B residue 264 GLU 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 C residue 69 GLU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain J residue 10 GLN Chi-restraints excluded: chain J residue 31 MET 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 267 optimal weight: 0.0870 chunk 272 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 304 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 116 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 HIS E 556 GLN E 713 HIS ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 ASN G 102 ASN A 92 ASN A 248 GLN A 278 GLN A 654 GLN B 504 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.120016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.097519 restraints weight = 37892.568| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.08 r_work: 0.3064 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25504 Z= 0.190 Angle : 0.635 10.002 34404 Z= 0.337 Chirality : 0.044 0.210 3769 Planarity : 0.005 0.057 4428 Dihedral : 4.931 50.251 3388 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.21 % Favored : 93.63 % Rotamer: Outliers : 4.65 % Allowed : 19.99 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 3077 helix: 1.20 (0.14), residues: 1534 sheet: 0.69 (0.34), residues: 219 loop : -2.40 (0.15), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 580 HIS 0.004 0.001 HIS F 47 PHE 0.040 0.002 PHE B 512 TYR 0.019 0.002 TYR F 30 ARG 0.006 0.000 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.07552 ( 1146) hydrogen bonds : angle 4.18510 ( 3258) covalent geometry : bond 0.00447 (25504) covalent geometry : angle 0.63457 (34404) *********************** 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 778 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 650 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 233 VAL cc_start: 0.9119 (OUTLIER) cc_final: 0.8903 (p) REVERT: E 262 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8458 (ttpp) REVERT: E 319 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7886 (mm-30) REVERT: E 347 ASP cc_start: 0.8154 (t70) cc_final: 0.7928 (t70) REVERT: E 430 GLU cc_start: 0.7640 (pm20) cc_final: 0.7385 (pm20) REVERT: E 512 ARG cc_start: 0.8299 (mtp85) cc_final: 0.7966 (mtp85) REVERT: E 532 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8129 (tt) REVERT: E 544 GLU cc_start: 0.8149 (tt0) cc_final: 0.7834 (tt0) REVERT: E 549 LEU cc_start: 0.8453 (mp) cc_final: 0.8225 (mp) REVERT: E 691 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8065 (mt-10) REVERT: F 104 GLU cc_start: 0.7564 (mp0) cc_final: 0.7071 (mp0) REVERT: F 120 ASP cc_start: 0.7383 (p0) cc_final: 0.7084 (p0) REVERT: F 141 THR cc_start: 0.8422 (p) cc_final: 0.8192 (m) REVERT: F 317 MET cc_start: 0.8568 (mmm) cc_final: 0.8346 (mpp) REVERT: F 387 LYS cc_start: 0.8279 (tttp) cc_final: 0.8061 (tttp) REVERT: F 398 ASP cc_start: 0.7983 (p0) cc_final: 0.7614 (p0) REVERT: F 442 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8246 (tt0) REVERT: F 475 ILE cc_start: 0.8245 (pt) cc_final: 0.7816 (mt) REVERT: F 571 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7394 (ttp80) REVERT: F 614 GLU cc_start: 0.7951 (pp20) cc_final: 0.7649 (pp20) REVERT: G 102 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8536 (p0) REVERT: A 16 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7819 (mt) REVERT: A 18 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: A 34 LYS cc_start: 0.7738 (mtpp) cc_final: 0.7315 (mttm) REVERT: A 65 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6360 (mm) REVERT: A 92 ASN cc_start: 0.7879 (m-40) cc_final: 0.7674 (m110) REVERT: A 95 CYS cc_start: 0.7120 (p) cc_final: 0.6808 (t) REVERT: A 101 GLU cc_start: 0.7429 (mp0) cc_final: 0.7106 (mp0) REVERT: A 114 GLU cc_start: 0.8210 (tp30) cc_final: 0.7647 (tp30) REVERT: A 128 HIS cc_start: 0.7454 (m-70) cc_final: 0.7100 (m-70) REVERT: A 129 ILE cc_start: 0.8647 (mm) cc_final: 0.8099 (mm) REVERT: A 181 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7470 (tm-30) REVERT: A 184 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.8168 (t0) REVERT: A 327 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6940 (pm20) REVERT: A 372 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6884 (mm-30) REVERT: A 380 ASP cc_start: 0.7747 (t70) cc_final: 0.7352 (p0) REVERT: A 382 ASP cc_start: 0.8090 (p0) cc_final: 0.7816 (p0) REVERT: A 385 ARG cc_start: 0.8320 (ptp-110) cc_final: 0.8021 (ttm-80) REVERT: A 469 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8743 (tt) REVERT: A 548 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8158 (ttm) REVERT: A 691 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8002 (mt-10) REVERT: A 693 CYS cc_start: 0.7596 (t) cc_final: 0.7350 (t) REVERT: A 712 THR cc_start: 0.8659 (t) cc_final: 0.8397 (m) REVERT: B 121 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7685 (tpp-160) REVERT: B 177 GLU cc_start: 0.7802 (tp30) cc_final: 0.7486 (tp30) REVERT: B 180 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7852 (mp0) REVERT: B 212 VAL cc_start: 0.8349 (OUTLIER) cc_final: 0.8053 (m) REVERT: B 264 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8195 (mt-10) REVERT: B 267 GLU cc_start: 0.7745 (pm20) cc_final: 0.7524 (pm20) REVERT: B 319 LEU cc_start: 0.8469 (tp) cc_final: 0.8210 (tt) REVERT: B 481 LYS cc_start: 0.8565 (mtmm) cc_final: 0.8328 (mtmm) REVERT: B 667 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8555 (mt) REVERT: B 687 GLN cc_start: 0.7847 (mp10) cc_final: 0.7635 (mp10) REVERT: B 694 ASN cc_start: 0.8366 (m110) cc_final: 0.8124 (m110) REVERT: B 751 GLU cc_start: 0.7866 (tt0) cc_final: 0.7661 (tt0) REVERT: C 46 ARG cc_start: 0.8197 (ttp-170) cc_final: 0.7944 (ttp-170) REVERT: C 69 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: C 116 LYS cc_start: 0.8558 (ptmm) cc_final: 0.8242 (ptmm) REVERT: C 158 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7142 (pm20) REVERT: C 171 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8053 (mt-10) REVERT: C 176 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7712 (tt) REVERT: C 177 LEU cc_start: 0.8382 (tt) cc_final: 0.8127 (tp) REVERT: C 735 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7550 (pp-130) REVERT: C 736 LYS cc_start: 0.8462 (tppp) cc_final: 0.8151 (tppp) REVERT: C 756 MET cc_start: 0.4355 (mpm) cc_final: 0.3337 (mpm) REVERT: I 50 MET cc_start: 0.7764 (ppp) cc_final: 0.7166 (ppp) REVERT: I 74 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7280 (mm-30) REVERT: I 81 GLU cc_start: 0.7716 (mp0) cc_final: 0.7510 (mp0) REVERT: I 100 MET cc_start: 0.7102 (mmp) cc_final: 0.6706 (mmt) REVERT: I 106 LEU cc_start: 0.7843 (mp) cc_final: 0.7454 (tp) REVERT: J 100 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7915 (mmm) outliers start: 128 outliers final: 53 residues processed: 700 average time/residue: 1.6523 time to fit residues: 1295.2282 Evaluate side-chains 709 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 630 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 233 VAL 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 532 LEU Chi-restraints excluded: chain E residue 587 GLN 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 E residue 692 GLU Chi-restraints excluded: chain F residue 41 ASP 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 172 GLU Chi-restraints excluded: chain F residue 179 MET 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 302 ILE Chi-restraints excluded: chain F residue 305 ASP Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 429 LYS Chi-restraints excluded: chain F residue 432 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 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 7 GLN Chi-restraints excluded: chain A residue 16 LEU 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 181 GLU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 372 GLU 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 595 MET Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 121 ARG 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 473 VAL Chi-restraints excluded: chain B residue 504 ASN Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 122 VAL 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 197 LYS Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 735 MET Chi-restraints excluded: chain J residue 10 GLN Chi-restraints excluded: chain J residue 31 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 121 optimal weight: 0.0000 chunk 264 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 287 optimal weight: 0.0970 chunk 272 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 143 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 220 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 238 optimal weight: 0.9990 overall best weight: 0.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 HIS F 58 ASN ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 ASN F 603 ASN G 102 ASN A 136 ASN A 654 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.122886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.100329 restraints weight = 37704.969| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.07 r_work: 0.3092 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25504 Z= 0.142 Angle : 0.591 9.438 34404 Z= 0.312 Chirality : 0.041 0.196 3769 Planarity : 0.005 0.051 4428 Dihedral : 4.650 46.311 3385 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.91 % Favored : 93.92 % Rotamer: Outliers : 4.87 % Allowed : 20.97 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 3077 helix: 1.40 (0.14), residues: 1520 sheet: 0.74 (0.34), residues: 219 loop : -2.34 (0.15), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 437 HIS 0.003 0.001 HIS F 47 PHE 0.029 0.001 PHE B 512 TYR 0.018 0.001 TYR F 30 ARG 0.004 0.000 ARG A 204 Details of bonding type rmsd hydrogen bonds : bond 0.06302 ( 1146) hydrogen bonds : angle 4.05430 ( 3258) covalent geometry : bond 0.00317 (25504) covalent geometry : angle 0.59072 (34404) *********************** 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 782 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 648 time to evaluate : 3.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 233 VAL cc_start: 0.9120 (t) cc_final: 0.8907 (p) REVERT: E 237 GLU cc_start: 0.8073 (tp30) cc_final: 0.7850 (tp30) REVERT: E 262 LYS cc_start: 0.8664 (ttmm) cc_final: 0.8211 (ttmm) REVERT: E 319 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7924 (mm-30) REVERT: E 321 TYR cc_start: 0.8812 (p90) cc_final: 0.8425 (p90) REVERT: E 347 ASP cc_start: 0.8110 (t70) cc_final: 0.7885 (t70) REVERT: E 351 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7272 (mt-10) REVERT: E 430 GLU cc_start: 0.7659 (pm20) cc_final: 0.7409 (pm20) REVERT: E 512 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7953 (mtp85) REVERT: E 532 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8094 (tt) REVERT: E 544 GLU cc_start: 0.8131 (tt0) cc_final: 0.7816 (tt0) REVERT: E 549 LEU cc_start: 0.8436 (mp) cc_final: 0.8212 (mp) REVERT: E 691 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8237 (mp0) REVERT: F 104 GLU cc_start: 0.7569 (mp0) cc_final: 0.7107 (mp0) REVERT: F 108 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8673 (mp) REVERT: F 120 ASP cc_start: 0.7344 (p0) cc_final: 0.7060 (p0) REVERT: F 141 THR cc_start: 0.8364 (p) cc_final: 0.8139 (m) REVERT: F 387 LYS cc_start: 0.8320 (tttp) cc_final: 0.8098 (tttp) REVERT: F 398 ASP cc_start: 0.8136 (p0) cc_final: 0.7774 (p0) REVERT: F 411 MET cc_start: 0.4685 (tmm) cc_final: 0.4146 (ppp) REVERT: F 442 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: F 475 ILE cc_start: 0.8203 (pt) cc_final: 0.7782 (mt) REVERT: F 571 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7340 (ttp80) REVERT: F 614 GLU cc_start: 0.7956 (pp20) cc_final: 0.7668 (pp20) REVERT: G 102 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8331 (p0) REVERT: A 18 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: A 34 LYS cc_start: 0.7624 (mtpp) cc_final: 0.7203 (mttm) REVERT: A 65 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6471 (mm) REVERT: A 95 CYS cc_start: 0.7054 (p) cc_final: 0.6699 (t) REVERT: A 114 GLU cc_start: 0.8242 (tp30) cc_final: 0.7692 (tp30) REVERT: A 122 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8625 (t) REVERT: A 126 GLU cc_start: 0.7085 (pp20) cc_final: 0.6847 (pp20) REVERT: A 128 HIS cc_start: 0.7460 (m-70) cc_final: 0.7108 (m-70) REVERT: A 129 ILE cc_start: 0.8568 (mm) cc_final: 0.7956 (mm) REVERT: A 133 GLU cc_start: 0.7799 (mp0) cc_final: 0.7410 (mp0) REVERT: A 170 ARG cc_start: 0.8310 (mtm-85) cc_final: 0.7898 (mtm-85) REVERT: A 181 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: A 327 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6918 (pm20) REVERT: A 372 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6581 (tp30) REVERT: A 380 ASP cc_start: 0.7803 (t70) cc_final: 0.7478 (p0) REVERT: A 382 ASP cc_start: 0.8185 (p0) cc_final: 0.7796 (p0) REVERT: A 385 ARG cc_start: 0.8272 (ptp-110) cc_final: 0.8051 (ttm-80) REVERT: A 469 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8694 (tt) REVERT: A 508 ARG cc_start: 0.7828 (mtt-85) cc_final: 0.7550 (mtm-85) REVERT: A 548 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8127 (ttm) REVERT: A 636 VAL cc_start: 0.7865 (OUTLIER) cc_final: 0.7547 (t) REVERT: A 691 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: A 693 CYS cc_start: 0.7557 (t) cc_final: 0.7269 (t) REVERT: B 151 ARG cc_start: 0.8582 (ppp80) cc_final: 0.8286 (ptm-80) REVERT: B 172 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7811 (mm-30) REVERT: B 177 GLU cc_start: 0.7879 (tp30) cc_final: 0.7618 (tp30) REVERT: B 212 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8114 (m) REVERT: B 264 GLU cc_start: 0.8392 (tp30) cc_final: 0.8165 (mt-10) REVERT: B 267 GLU cc_start: 0.7745 (pm20) cc_final: 0.7502 (pm20) REVERT: B 307 THR cc_start: 0.8589 (t) cc_final: 0.8370 (t) REVERT: B 386 ARG cc_start: 0.8166 (mtp-110) cc_final: 0.7639 (ttm-80) REVERT: B 481 LYS cc_start: 0.8581 (mtmm) cc_final: 0.8293 (mtmm) REVERT: B 504 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8107 (p0) REVERT: B 667 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8561 (mt) REVERT: B 687 GLN cc_start: 0.7808 (mp10) cc_final: 0.7584 (mp10) REVERT: B 694 ASN cc_start: 0.8387 (m110) cc_final: 0.8152 (m110) REVERT: B 751 GLU cc_start: 0.7889 (tt0) cc_final: 0.7669 (tt0) REVERT: C 46 ARG cc_start: 0.8198 (ttp-170) cc_final: 0.7941 (ttp-170) REVERT: C 116 LYS cc_start: 0.8557 (ptmm) cc_final: 0.8240 (ptmm) REVERT: C 158 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7170 (pm20) REVERT: C 171 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8018 (mt-10) REVERT: C 176 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7634 (tt) REVERT: C 177 LEU cc_start: 0.8361 (tt) cc_final: 0.8109 (tp) REVERT: C 699 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7840 (mtpt) REVERT: C 735 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7569 (pp-130) REVERT: C 736 LYS cc_start: 0.8545 (tppp) cc_final: 0.8206 (tppp) REVERT: C 756 MET cc_start: 0.4136 (mpm) cc_final: 0.2875 (mpm) REVERT: I 40 LEU cc_start: 0.7419 (mt) cc_final: 0.7163 (mm) REVERT: I 50 MET cc_start: 0.7788 (ppp) cc_final: 0.7148 (ppp) REVERT: I 74 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7691 (mm-30) REVERT: I 106 LEU cc_start: 0.7836 (mp) cc_final: 0.7431 (tp) REVERT: J 100 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7945 (mmm) outliers start: 134 outliers final: 64 residues processed: 703 average time/residue: 1.6727 time to fit residues: 1315.6017 Evaluate side-chains 734 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 645 time to evaluate : 2.615 ------------------------------------------------------------------------------- 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 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 516 ASP Chi-restraints excluded: chain E residue 532 LEU Chi-restraints excluded: chain E residue 608 THR 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 108 LEU 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 171 MET 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 391 LYS 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 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 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 163 LEU Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 372 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 491 THR 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 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 61 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 171 MET 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 302 ILE Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 504 ASN 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 122 VAL 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 193 LEU Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 699 LYS Chi-restraints excluded: chain C residue 723 ASN Chi-restraints excluded: chain C residue 735 MET Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain J residue 10 GLN Chi-restraints excluded: chain J residue 31 MET 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 110 optimal weight: 0.2980 chunk 53 optimal weight: 0.6980 chunk 290 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 182 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 292 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 41 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 HIS ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 ASN F 603 ASN G 102 ASN A 92 ASN A 136 ASN A 180 GLN A 654 GLN I 20 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.122259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.099630 restraints weight = 37560.973| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.07 r_work: 0.3082 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25504 Z= 0.156 Angle : 0.603 9.374 34404 Z= 0.318 Chirality : 0.042 0.204 3769 Planarity : 0.005 0.054 4428 Dihedral : 4.598 43.864 3385 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.21 % Favored : 93.63 % Rotamer: Outliers : 5.12 % Allowed : 21.29 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 3077 helix: 1.39 (0.14), residues: 1531 sheet: 0.61 (0.34), residues: 230 loop : -2.35 (0.15), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 78 HIS 0.004 0.001 HIS F 47 PHE 0.029 0.001 PHE B 512 TYR 0.018 0.001 TYR F 30 ARG 0.004 0.000 ARG F 334 Details of bonding type rmsd hydrogen bonds : bond 0.06637 ( 1146) hydrogen bonds : angle 4.05081 ( 3258) covalent geometry : bond 0.00357 (25504) covalent geometry : angle 0.60259 (34404) *********************** 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 805 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 664 time to evaluate : 2.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 233 VAL cc_start: 0.9125 (t) cc_final: 0.8916 (p) REVERT: E 262 LYS cc_start: 0.8642 (ttmm) cc_final: 0.8424 (ttpp) REVERT: E 319 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7948 (mm-30) REVERT: E 347 ASP cc_start: 0.8141 (t70) cc_final: 0.7933 (t70) REVERT: E 512 ARG cc_start: 0.8223 (mtp85) cc_final: 0.7901 (mtp85) REVERT: E 544 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7832 (tt0) REVERT: E 549 LEU cc_start: 0.8468 (mp) cc_final: 0.8240 (mp) REVERT: E 691 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8052 (mt-10) REVERT: F 104 GLU cc_start: 0.7590 (mp0) cc_final: 0.7165 (mp0) REVERT: F 120 ASP cc_start: 0.7333 (p0) cc_final: 0.7072 (p0) REVERT: F 398 ASP cc_start: 0.8126 (p0) cc_final: 0.7759 (p0) REVERT: F 411 MET cc_start: 0.4722 (tmm) cc_final: 0.4252 (ppp) REVERT: F 442 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: F 475 ILE cc_start: 0.8212 (pt) cc_final: 0.7782 (mt) REVERT: F 571 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7377 (ttp80) REVERT: F 614 GLU cc_start: 0.7978 (pp20) cc_final: 0.7708 (pp20) REVERT: A 18 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: A 34 LYS cc_start: 0.7630 (mtpp) cc_final: 0.7217 (mttm) REVERT: A 65 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6536 (mm) REVERT: A 92 ASN cc_start: 0.7810 (m-40) cc_final: 0.7609 (m110) REVERT: A 95 CYS cc_start: 0.7065 (p) cc_final: 0.6715 (t) REVERT: A 101 GLU cc_start: 0.7399 (mp0) cc_final: 0.7057 (mp0) REVERT: A 110 TYR cc_start: 0.7914 (t80) cc_final: 0.7694 (t80) REVERT: A 114 GLU cc_start: 0.8234 (tp30) cc_final: 0.7660 (tp30) REVERT: A 126 GLU cc_start: 0.7151 (pp20) cc_final: 0.6878 (pp20) REVERT: A 128 HIS cc_start: 0.7414 (m-70) cc_final: 0.7080 (m-70) REVERT: A 129 ILE cc_start: 0.8569 (mm) cc_final: 0.8143 (mm) REVERT: A 153 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7691 (mm-30) REVERT: A 170 ARG cc_start: 0.8325 (mtm-85) cc_final: 0.7925 (mtm-85) REVERT: A 181 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7522 (tm-30) REVERT: A 272 ASP cc_start: 0.8211 (p0) cc_final: 0.7955 (p0) REVERT: A 327 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6919 (pm20) REVERT: A 372 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6510 (tp30) REVERT: A 374 MET cc_start: 0.7116 (mpp) cc_final: 0.6860 (mpp) REVERT: A 380 ASP cc_start: 0.7759 (t70) cc_final: 0.6873 (t70) REVERT: A 382 ASP cc_start: 0.8119 (p0) cc_final: 0.7874 (p0) REVERT: A 469 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8688 (tt) REVERT: A 508 ARG cc_start: 0.7864 (mtt-85) cc_final: 0.7559 (mtm-85) REVERT: A 548 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8108 (ttm) REVERT: A 636 VAL cc_start: 0.7894 (OUTLIER) cc_final: 0.7591 (t) REVERT: A 691 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: A 693 CYS cc_start: 0.7601 (t) cc_final: 0.7285 (t) REVERT: A 712 THR cc_start: 0.8591 (t) cc_final: 0.8301 (m) REVERT: B 90 GLU cc_start: 0.8387 (tt0) cc_final: 0.8179 (tt0) REVERT: B 96 GLU cc_start: 0.8390 (tp30) cc_final: 0.8048 (tp30) REVERT: B 121 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7673 (tpp-160) REVERT: B 172 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7875 (mm-30) REVERT: B 177 GLU cc_start: 0.7884 (tp30) cc_final: 0.7666 (tp30) REVERT: B 178 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7676 (mt-10) REVERT: B 212 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8221 (m) REVERT: B 260 ARG cc_start: 0.8644 (ttt90) cc_final: 0.8404 (ttt90) REVERT: B 267 GLU cc_start: 0.7736 (pm20) cc_final: 0.7504 (pm20) REVERT: B 287 ARG cc_start: 0.8525 (tmm-80) cc_final: 0.8132 (ttm-80) REVERT: B 307 THR cc_start: 0.8573 (t) cc_final: 0.8361 (t) REVERT: B 481 LYS cc_start: 0.8582 (mtmm) cc_final: 0.8222 (mtmm) REVERT: B 667 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8566 (mt) REVERT: B 687 GLN cc_start: 0.7852 (mp10) cc_final: 0.7614 (mp10) REVERT: B 694 ASN cc_start: 0.8407 (m110) cc_final: 0.8183 (m110) REVERT: B 751 GLU cc_start: 0.7938 (tt0) cc_final: 0.7721 (tt0) REVERT: C 46 ARG cc_start: 0.8185 (ttp-170) cc_final: 0.7931 (ttp-170) REVERT: C 116 LYS cc_start: 0.8622 (ptmm) cc_final: 0.8307 (ptmm) REVERT: C 158 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7212 (pm20) REVERT: C 171 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: C 176 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7674 (tt) REVERT: C 177 LEU cc_start: 0.8393 (tt) cc_final: 0.8136 (tp) REVERT: C 699 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7907 (mtpt) REVERT: C 735 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7702 (ppp) REVERT: C 736 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8243 (tptm) REVERT: C 756 MET cc_start: 0.3978 (mpm) cc_final: 0.2687 (mpm) REVERT: I 40 LEU cc_start: 0.7460 (mt) cc_final: 0.7214 (mm) REVERT: I 50 MET cc_start: 0.7892 (ppp) cc_final: 0.7192 (ppp) REVERT: I 74 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7681 (mm-30) REVERT: I 87 LEU cc_start: 0.7939 (tm) cc_final: 0.7661 (tt) REVERT: I 106 LEU cc_start: 0.7830 (mp) cc_final: 0.7427 (tp) REVERT: J 100 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7936 (mmm) outliers start: 141 outliers final: 75 residues processed: 718 average time/residue: 1.6714 time to fit residues: 1351.1105 Evaluate side-chains 749 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 650 time to evaluate : 2.836 ------------------------------------------------------------------------------- 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 450 VAL Chi-restraints excluded: chain E residue 473 SER 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 570 THR Chi-restraints excluded: chain E residue 587 GLN Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 613 GLU 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 60 GLU Chi-restraints excluded: chain F residue 69 ILE 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 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 267 GLU Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 408 MET 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 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 153 GLU Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 372 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 491 THR 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 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 61 THR Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 171 MET 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 473 VAL 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 158 GLU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 699 LYS Chi-restraints excluded: chain C residue 723 ASN Chi-restraints excluded: chain C residue 735 MET Chi-restraints excluded: chain C residue 736 LYS Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain J residue 10 GLN Chi-restraints excluded: chain J residue 31 MET 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 199 optimal weight: 1.9990 chunk 250 optimal weight: 0.1980 chunk 6 optimal weight: 0.9990 chunk 281 optimal weight: 0.0770 chunk 59 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 chunk 290 optimal weight: 0.9980 chunk 287 optimal weight: 0.2980 chunk 128 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 overall best weight: 0.2938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 HIS ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 ASN F 603 ASN A 136 ASN A 452 HIS A 654 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.124312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.101732 restraints weight = 37701.059| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.08 r_work: 0.3121 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25504 Z= 0.124 Angle : 0.564 8.606 34404 Z= 0.297 Chirality : 0.040 0.198 3769 Planarity : 0.004 0.046 4428 Dihedral : 4.407 41.518 3385 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.62 % Favored : 94.28 % Rotamer: Outliers : 4.51 % Allowed : 22.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3077 helix: 1.55 (0.14), residues: 1523 sheet: 0.44 (0.34), residues: 232 loop : -2.29 (0.15), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 65 HIS 0.003 0.000 HIS F 47 PHE 0.026 0.001 PHE I 116 TYR 0.017 0.001 TYR F 30 ARG 0.004 0.000 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.05356 ( 1146) hydrogen bonds : angle 3.91640 ( 3258) covalent geometry : bond 0.00272 (25504) covalent geometry : angle 0.56381 (34404) *********************** 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 789 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 665 time to evaluate : 2.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 229 PHE cc_start: 0.6089 (m-80) cc_final: 0.4462 (t80) REVERT: E 262 LYS cc_start: 0.8594 (ttmm) cc_final: 0.8382 (ttpp) REVERT: E 321 TYR cc_start: 0.8814 (p90) cc_final: 0.8446 (p90) REVERT: E 430 GLU cc_start: 0.7684 (pm20) cc_final: 0.7438 (pm20) REVERT: E 512 ARG cc_start: 0.8265 (mtp85) cc_final: 0.7961 (mtp85) REVERT: E 544 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: E 549 LEU cc_start: 0.8383 (mp) cc_final: 0.8137 (mp) REVERT: E 691 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8013 (mt-10) REVERT: F 104 GLU cc_start: 0.7550 (mp0) cc_final: 0.7125 (mp0) REVERT: F 120 ASP cc_start: 0.7245 (p0) cc_final: 0.6989 (p0) REVERT: F 132 THR cc_start: 0.8902 (m) cc_final: 0.8446 (p) REVERT: F 260 ARG cc_start: 0.8417 (mtp-110) cc_final: 0.8131 (mmm-85) REVERT: F 398 ASP cc_start: 0.8198 (p0) cc_final: 0.7835 (p0) REVERT: F 411 MET cc_start: 0.4626 (tmm) cc_final: 0.4125 (ppp) REVERT: F 442 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: F 475 ILE cc_start: 0.8156 (pt) cc_final: 0.7746 (mt) REVERT: F 614 GLU cc_start: 0.7985 (pp20) cc_final: 0.7761 (pp20) REVERT: G 100 ASN cc_start: 0.8812 (m-40) cc_final: 0.8604 (m110) REVERT: A 18 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: A 34 LYS cc_start: 0.7524 (mtpp) cc_final: 0.7108 (mttm) REVERT: A 65 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6524 (mm) REVERT: A 95 CYS cc_start: 0.7095 (p) cc_final: 0.6788 (t) REVERT: A 101 GLU cc_start: 0.7442 (mp0) cc_final: 0.7099 (mp0) REVERT: A 114 GLU cc_start: 0.8143 (tp30) cc_final: 0.7553 (tp30) REVERT: A 122 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8589 (t) REVERT: A 126 GLU cc_start: 0.7187 (pp20) cc_final: 0.6886 (pp20) REVERT: A 128 HIS cc_start: 0.7392 (m-70) cc_final: 0.7102 (m-70) REVERT: A 129 ILE cc_start: 0.8524 (mm) cc_final: 0.8086 (mm) REVERT: A 133 GLU cc_start: 0.7754 (mp0) cc_final: 0.7487 (mm-30) REVERT: A 170 ARG cc_start: 0.8205 (mtm-85) cc_final: 0.7828 (mtm-85) REVERT: A 179 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8519 (tmt170) REVERT: A 181 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7476 (tm-30) REVERT: A 272 ASP cc_start: 0.8164 (p0) cc_final: 0.7909 (p0) REVERT: A 327 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6769 (pm20) REVERT: A 372 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6389 (tp30) REVERT: A 374 MET cc_start: 0.7124 (mpp) cc_final: 0.6888 (mpp) REVERT: A 385 ARG cc_start: 0.8010 (ttm-80) cc_final: 0.7666 (ttm-80) REVERT: A 450 VAL cc_start: 0.8235 (OUTLIER) cc_final: 0.8012 (p) REVERT: A 469 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8656 (tt) REVERT: A 508 ARG cc_start: 0.7841 (mtt-85) cc_final: 0.7507 (mtm-85) REVERT: A 548 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.8110 (ttm) REVERT: A 691 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7862 (mt-10) REVERT: A 693 CYS cc_start: 0.7544 (t) cc_final: 0.7248 (t) REVERT: B 96 GLU cc_start: 0.8375 (tp30) cc_final: 0.8040 (tp30) REVERT: B 172 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7844 (mm-30) REVERT: B 177 GLU cc_start: 0.7959 (tp30) cc_final: 0.7677 (tp30) REVERT: B 212 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8171 (m) REVERT: B 267 GLU cc_start: 0.7698 (pm20) cc_final: 0.7462 (pm20) REVERT: B 287 ARG cc_start: 0.8493 (tmm-80) cc_final: 0.8120 (ttm-80) REVERT: B 307 THR cc_start: 0.8556 (t) cc_final: 0.8341 (t) REVERT: B 362 MET cc_start: 0.8374 (mpm) cc_final: 0.8088 (mpt) REVERT: B 481 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8302 (mtmm) REVERT: B 584 ARG cc_start: 0.8129 (ttm-80) cc_final: 0.7894 (ttm-80) REVERT: B 667 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8575 (mt) REVERT: B 694 ASN cc_start: 0.8384 (m110) cc_final: 0.8154 (m110) REVERT: B 709 VAL cc_start: 0.8836 (t) cc_final: 0.8554 (m) REVERT: B 751 GLU cc_start: 0.7886 (tt0) cc_final: 0.7673 (tt0) REVERT: C 46 ARG cc_start: 0.8171 (ttp-170) cc_final: 0.7939 (ttp-170) REVERT: C 158 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7186 (pm20) REVERT: C 171 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: C 176 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7596 (tt) REVERT: C 177 LEU cc_start: 0.8376 (tt) cc_final: 0.8120 (tp) REVERT: C 187 LYS cc_start: 0.8006 (ttpp) cc_final: 0.7712 (ttpp) REVERT: C 721 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8197 (ptpt) REVERT: C 735 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7718 (ppp) REVERT: C 736 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8260 (tppp) REVERT: C 756 MET cc_start: 0.4063 (mpm) cc_final: 0.2744 (mpm) REVERT: I 40 LEU cc_start: 0.7471 (mt) cc_final: 0.7224 (mm) REVERT: I 50 MET cc_start: 0.7799 (ppp) cc_final: 0.7068 (ppp) REVERT: I 68 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6412 (mp10) REVERT: I 74 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7169 (mm-30) REVERT: I 81 GLU cc_start: 0.7665 (mp0) cc_final: 0.7415 (mp0) REVERT: I 106 LEU cc_start: 0.7770 (mp) cc_final: 0.7351 (tp) REVERT: J 100 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7882 (mmm) outliers start: 124 outliers final: 62 residues processed: 715 average time/residue: 1.7137 time to fit residues: 1368.8381 Evaluate side-chains 734 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 648 time to evaluate : 2.955 ------------------------------------------------------------------------------- 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 431 ASP Chi-restraints excluded: chain E residue 544 GLU Chi-restraints excluded: chain E residue 570 THR Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 613 GLU Chi-restraints excluded: chain E residue 618 THR 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 55 TRP Chi-restraints excluded: chain F residue 60 GLU 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 172 GLU 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 408 MET 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 534 MET Chi-restraints excluded: chain F residue 592 SER Chi-restraints excluded: chain F residue 618 GLU 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 65 LEU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 115 ASN 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 181 GLU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 372 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 478 ASP Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 557 MET 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 112 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 212 VAL Chi-restraints excluded: chain B residue 218 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 628 LEU Chi-restraints excluded: chain B residue 667 ILE 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 213 ARG Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 721 LYS Chi-restraints excluded: chain C residue 723 ASN Chi-restraints excluded: chain C residue 735 MET Chi-restraints excluded: chain C residue 736 LYS Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain J residue 10 GLN Chi-restraints excluded: chain J residue 31 MET 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 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 224 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 259 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 HIS ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 276 ASN F 533 ASN A 92 ASN A 136 ASN A 346 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.119102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.096441 restraints weight = 37445.625| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.07 r_work: 0.3031 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 25504 Z= 0.230 Angle : 0.687 9.846 34404 Z= 0.362 Chirality : 0.046 0.220 3769 Planarity : 0.005 0.059 4428 Dihedral : 4.789 41.303 3385 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.63 % Favored : 93.21 % Rotamer: Outliers : 4.83 % Allowed : 22.82 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 3077 helix: 1.29 (0.14), residues: 1533 sheet: 0.56 (0.35), residues: 221 loop : -2.39 (0.15), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 55 HIS 0.006 0.001 HIS E 326 PHE 0.035 0.002 PHE B 512 TYR 0.018 0.002 TYR F 555 ARG 0.005 0.001 ARG F 334 Details of bonding type rmsd hydrogen bonds : bond 0.08501 ( 1146) hydrogen bonds : angle 4.24600 ( 3258) covalent geometry : bond 0.00553 (25504) covalent geometry : angle 0.68696 (34404) *********************** 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 790 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 657 time to evaluate : 2.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 360 MET cc_start: 0.8738 (mmm) cc_final: 0.8503 (mmt) REVERT: E 473 SER cc_start: 0.8931 (OUTLIER) cc_final: 0.8650 (m) REVERT: E 512 ARG cc_start: 0.8281 (mtp85) cc_final: 0.8012 (mtp85) REVERT: E 544 GLU cc_start: 0.8173 (tt0) cc_final: 0.7868 (tt0) REVERT: E 549 LEU cc_start: 0.8442 (mp) cc_final: 0.8196 (mp) REVERT: E 594 SER cc_start: 0.8627 (t) cc_final: 0.8384 (m) REVERT: E 623 GLU cc_start: 0.7992 (tp30) cc_final: 0.7494 (tt0) REVERT: E 691 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: F 104 GLU cc_start: 0.7591 (mp0) cc_final: 0.7159 (mp0) REVERT: F 120 ASP cc_start: 0.7535 (p0) cc_final: 0.7273 (p0) REVERT: F 132 THR cc_start: 0.8863 (m) cc_final: 0.8418 (p) REVERT: F 179 MET cc_start: 0.5080 (ppp) cc_final: 0.4605 (ptm) REVERT: F 376 ILE cc_start: 0.8063 (mm) cc_final: 0.7808 (mm) REVERT: F 398 ASP cc_start: 0.8161 (p0) cc_final: 0.7798 (p0) REVERT: F 411 MET cc_start: 0.4825 (tmm) cc_final: 0.4356 (ppp) REVERT: F 442 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: F 457 GLU cc_start: 0.8069 (mp0) cc_final: 0.7750 (mp0) REVERT: F 475 ILE cc_start: 0.8260 (pt) cc_final: 0.7844 (mt) REVERT: F 571 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7526 (ttp80) REVERT: F 614 GLU cc_start: 0.8005 (pp20) cc_final: 0.7729 (pp20) REVERT: A 8 CYS cc_start: 0.8519 (t) cc_final: 0.8224 (t) REVERT: A 18 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: A 34 LYS cc_start: 0.7696 (mtpp) cc_final: 0.7306 (mttm) REVERT: A 113 LYS cc_start: 0.8616 (tttm) cc_final: 0.8329 (ttpp) REVERT: A 114 GLU cc_start: 0.8183 (tp30) cc_final: 0.7561 (tp30) REVERT: A 126 GLU cc_start: 0.7383 (pp20) cc_final: 0.7096 (pp20) REVERT: A 127 VAL cc_start: 0.8308 (t) cc_final: 0.8059 (p) REVERT: A 128 HIS cc_start: 0.7489 (m-70) cc_final: 0.7207 (m-70) REVERT: A 129 ILE cc_start: 0.8511 (mm) cc_final: 0.8230 (mp) REVERT: A 153 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7683 (mm-30) REVERT: A 184 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8276 (t0) REVERT: A 272 ASP cc_start: 0.8199 (p0) cc_final: 0.7927 (p0) REVERT: A 327 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6922 (pm20) REVERT: A 372 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6683 (tp30) REVERT: A 374 MET cc_start: 0.7155 (mpp) cc_final: 0.6888 (mpp) REVERT: A 469 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8773 (tt) REVERT: A 508 ARG cc_start: 0.7881 (mtt-85) cc_final: 0.7590 (mtt-85) REVERT: A 549 LEU cc_start: 0.8663 (mp) cc_final: 0.8409 (mm) REVERT: A 636 VAL cc_start: 0.7989 (OUTLIER) cc_final: 0.7771 (t) REVERT: A 691 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: B 75 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8194 (mt-10) REVERT: B 96 GLU cc_start: 0.8439 (tp30) cc_final: 0.8095 (tp30) REVERT: B 121 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7692 (tpp-160) REVERT: B 172 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7896 (mm-30) REVERT: B 177 GLU cc_start: 0.8016 (tp30) cc_final: 0.7685 (tp30) REVERT: B 178 GLU cc_start: 0.8234 (mt-10) cc_final: 0.8029 (tt0) REVERT: B 212 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8321 (m) REVERT: B 260 ARG cc_start: 0.8661 (ttt90) cc_final: 0.8387 (ttt90) REVERT: B 267 GLU cc_start: 0.7726 (pm20) cc_final: 0.7509 (pm20) REVERT: B 362 MET cc_start: 0.8421 (mpm) cc_final: 0.8146 (mpt) REVERT: B 481 LYS cc_start: 0.8650 (mtmm) cc_final: 0.8295 (mtmm) REVERT: B 584 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7964 (ttm-80) REVERT: B 667 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8597 (mt) REVERT: B 751 GLU cc_start: 0.7945 (tt0) cc_final: 0.7727 (tt0) REVERT: C 46 ARG cc_start: 0.8239 (ttp-170) cc_final: 0.7997 (ttp-170) REVERT: C 69 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: C 158 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7223 (pm20) REVERT: C 171 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8033 (mt-10) REVERT: C 176 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7821 (tt) REVERT: C 177 LEU cc_start: 0.8486 (tt) cc_final: 0.8197 (tp) REVERT: C 188 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: C 216 ARG cc_start: 0.7049 (mtt180) cc_final: 0.6815 (mtt90) REVERT: C 699 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7859 (mtpt) REVERT: C 756 MET cc_start: 0.4476 (mpm) cc_final: 0.3453 (mpm) REVERT: I 40 LEU cc_start: 0.7559 (mt) cc_final: 0.7333 (mm) REVERT: I 50 MET cc_start: 0.7979 (ppp) cc_final: 0.7226 (ppp) REVERT: I 68 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6461 (mp10) REVERT: I 74 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7667 (mm-30) REVERT: I 81 GLU cc_start: 0.7738 (mp0) cc_final: 0.7449 (mp0) REVERT: I 113 ILE cc_start: 0.8641 (mt) cc_final: 0.8331 (mp) outliers start: 133 outliers final: 73 residues processed: 714 average time/residue: 1.7132 time to fit residues: 1365.3073 Evaluate side-chains 757 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 662 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 247 SER 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 473 SER Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain E residue 570 THR Chi-restraints excluded: chain E residue 597 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 60 GLU Chi-restraints excluded: chain F residue 108 LEU 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 172 GLU Chi-restraints excluded: chain F residue 215 ARG 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 408 MET 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 534 MET Chi-restraints excluded: chain F residue 571 ARG Chi-restraints excluded: chain F residue 592 SER 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 145 ILE Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 312 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 372 GLU Chi-restraints excluded: chain A residue 386 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 558 SER 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 112 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 122 VAL 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 213 ARG Chi-restraints excluded: chain C residue 699 LYS Chi-restraints excluded: chain C residue 721 LYS Chi-restraints excluded: chain C residue 723 ASN Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain J residue 10 GLN Chi-restraints excluded: chain J residue 29 ASN Chi-restraints excluded: chain J residue 31 MET 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 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 217 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 224 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 285 optimal weight: 1.9990 chunk 129 optimal weight: 0.3980 chunk 99 optimal weight: 0.6980 chunk 203 optimal weight: 0.6980 chunk 248 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 299 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 HIS F 328 ASN A 92 ASN A 136 ASN A 654 GLN B 569 GLN B 687 GLN B 694 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.120704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.098283 restraints weight = 37569.465| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.05 r_work: 0.3065 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25504 Z= 0.173 Angle : 0.644 12.000 34404 Z= 0.337 Chirality : 0.043 0.204 3769 Planarity : 0.005 0.055 4428 Dihedral : 4.683 39.135 3385 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.95 % Favored : 93.89 % Rotamer: Outliers : 4.14 % Allowed : 23.73 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 3077 helix: 1.38 (0.14), residues: 1527 sheet: 0.59 (0.35), residues: 223 loop : -2.40 (0.15), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 55 HIS 0.004 0.001 HIS F 47 PHE 0.031 0.002 PHE I 116 TYR 0.018 0.001 TYR F 30 ARG 0.006 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.07029 ( 1146) hydrogen bonds : angle 4.11815 ( 3258) covalent geometry : bond 0.00402 (25504) covalent geometry : angle 0.64389 (34404) *********************** 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 769 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 655 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 321 TYR cc_start: 0.8817 (p90) cc_final: 0.8434 (p90) REVERT: E 512 ARG cc_start: 0.8330 (mtp85) cc_final: 0.8104 (mtp85) REVERT: E 544 GLU cc_start: 0.8178 (tt0) cc_final: 0.7866 (tt0) REVERT: E 549 LEU cc_start: 0.8429 (mp) cc_final: 0.8187 (mp) REVERT: E 594 SER cc_start: 0.8645 (t) cc_final: 0.8392 (m) REVERT: E 623 GLU cc_start: 0.7978 (tp30) cc_final: 0.7569 (tt0) REVERT: E 691 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8071 (mt-10) REVERT: F 104 GLU cc_start: 0.7577 (mp0) cc_final: 0.7163 (mp0) REVERT: F 117 THR cc_start: 0.8531 (t) cc_final: 0.8222 (m) REVERT: F 120 ASP cc_start: 0.7527 (p0) cc_final: 0.7254 (p0) REVERT: F 132 THR cc_start: 0.8859 (m) cc_final: 0.8405 (p) REVERT: F 155 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8520 (mt) REVERT: F 179 MET cc_start: 0.5047 (ppp) cc_final: 0.4546 (ptm) REVERT: F 288 LYS cc_start: 0.8487 (tttm) cc_final: 0.8164 (ttmm) REVERT: F 376 ILE cc_start: 0.8045 (mm) cc_final: 0.7600 (mp) REVERT: F 398 ASP cc_start: 0.8210 (p0) cc_final: 0.7836 (p0) REVERT: F 411 MET cc_start: 0.4790 (tmm) cc_final: 0.4334 (ppp) REVERT: F 442 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: F 457 GLU cc_start: 0.7959 (mp0) cc_final: 0.7651 (mp0) REVERT: F 475 ILE cc_start: 0.8217 (pt) cc_final: 0.7787 (mt) REVERT: F 485 ASN cc_start: 0.7922 (m-40) cc_final: 0.7495 (m-40) REVERT: F 571 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7434 (ttp80) REVERT: F 614 GLU cc_start: 0.8002 (pp20) cc_final: 0.7733 (pp20) REVERT: A 8 CYS cc_start: 0.8539 (t) cc_final: 0.8241 (t) REVERT: A 18 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: A 34 LYS cc_start: 0.7611 (mtpp) cc_final: 0.7215 (mttm) REVERT: A 113 LYS cc_start: 0.8629 (tttm) cc_final: 0.8358 (ttpp) REVERT: A 114 GLU cc_start: 0.8160 (tp30) cc_final: 0.7594 (tp30) REVERT: A 117 PHE cc_start: 0.7758 (m-10) cc_final: 0.7192 (m-80) REVERT: A 126 GLU cc_start: 0.7389 (pp20) cc_final: 0.7144 (pp20) REVERT: A 128 HIS cc_start: 0.7441 (m-70) cc_final: 0.7157 (m-70) REVERT: A 129 ILE cc_start: 0.8521 (mm) cc_final: 0.8270 (mp) REVERT: A 153 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7687 (mm-30) REVERT: A 170 ARG cc_start: 0.8375 (mmm-85) cc_final: 0.7999 (mtm-85) REVERT: A 272 ASP cc_start: 0.8174 (p0) cc_final: 0.7909 (p0) REVERT: A 327 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6883 (pm20) REVERT: A 372 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.7080 (tp30) REVERT: A 374 MET cc_start: 0.7146 (mpp) cc_final: 0.6899 (mpp) REVERT: A 469 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8736 (tt) REVERT: A 548 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8115 (ttm) REVERT: A 549 LEU cc_start: 0.8692 (mp) cc_final: 0.8443 (mm) REVERT: A 636 VAL cc_start: 0.7918 (OUTLIER) cc_final: 0.7563 (t) REVERT: A 691 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7933 (mt-10) REVERT: B 96 GLU cc_start: 0.8400 (tp30) cc_final: 0.8070 (tp30) REVERT: B 177 GLU cc_start: 0.8014 (tp30) cc_final: 0.7606 (tp30) REVERT: B 178 GLU cc_start: 0.8234 (mt-10) cc_final: 0.8008 (tt0) REVERT: B 212 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8327 (m) REVERT: B 260 ARG cc_start: 0.8632 (ttt90) cc_final: 0.8340 (ttt90) REVERT: B 267 GLU cc_start: 0.7677 (pm20) cc_final: 0.7473 (pm20) REVERT: B 287 ARG cc_start: 0.8516 (tmm-80) cc_final: 0.8141 (ttm-80) REVERT: B 290 MET cc_start: 0.7478 (tpt) cc_final: 0.7229 (mmp) REVERT: B 362 MET cc_start: 0.8390 (mpm) cc_final: 0.8097 (mpt) REVERT: B 481 LYS cc_start: 0.8603 (mtmm) cc_final: 0.8243 (mtmm) REVERT: B 584 ARG cc_start: 0.8170 (ttm-80) cc_final: 0.7932 (ttm-80) REVERT: B 667 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8575 (mt) REVERT: B 709 VAL cc_start: 0.8810 (t) cc_final: 0.8605 (m) REVERT: B 751 GLU cc_start: 0.7908 (tt0) cc_final: 0.7700 (tt0) REVERT: C 22 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8100 (mttt) REVERT: C 46 ARG cc_start: 0.8231 (ttp-170) cc_final: 0.7993 (ttp-170) REVERT: C 158 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7220 (pm20) REVERT: C 171 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: C 176 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7777 (tt) REVERT: C 177 LEU cc_start: 0.8444 (tt) cc_final: 0.8159 (tp) REVERT: C 187 LYS cc_start: 0.8122 (ttpp) cc_final: 0.7840 (ttpp) REVERT: C 188 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7341 (mt-10) REVERT: C 756 MET cc_start: 0.4315 (mpm) cc_final: 0.3362 (mpm) REVERT: I 40 LEU cc_start: 0.7557 (mt) cc_final: 0.7344 (mm) REVERT: I 50 MET cc_start: 0.8015 (ppp) cc_final: 0.7247 (ppp) REVERT: I 68 GLN cc_start: 0.7181 (OUTLIER) cc_final: 0.6428 (mp10) REVERT: I 74 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7607 (mm-30) REVERT: I 81 GLU cc_start: 0.7799 (mp0) cc_final: 0.7450 (mp0) REVERT: I 113 ILE cc_start: 0.8641 (mt) cc_final: 0.8350 (mp) outliers start: 114 outliers final: 76 residues processed: 703 average time/residue: 1.6834 time to fit residues: 1330.2863 Evaluate side-chains 748 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 652 time to evaluate : 2.987 ------------------------------------------------------------------------------- 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 473 SER Chi-restraints excluded: chain E residue 570 THR 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 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 124 GLN Chi-restraints excluded: chain F residue 148 GLU Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 155 LEU 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 391 LYS Chi-restraints excluded: chain F residue 408 MET 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 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 145 ILE Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 312 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 372 GLU Chi-restraints excluded: chain A residue 386 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 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 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 112 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 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 473 VAL 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 122 VAL 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 213 ARG Chi-restraints excluded: chain C residue 723 ASN Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain J residue 10 GLN Chi-restraints excluded: chain J residue 29 ASN Chi-restraints excluded: chain J residue 31 MET 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 103 LEU Chi-restraints excluded: chain J residue 105 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 18 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 252 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 254 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 239 optimal weight: 0.0020 chunk 31 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 74 optimal weight: 0.0670 overall best weight: 0.4726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 328 ASN A 92 ASN A 136 ASN A 654 GLN B 694 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.095946 restraints weight = 37431.978| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.03 r_work: 0.3081 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25504 Z= 0.155 Angle : 0.635 10.988 34404 Z= 0.331 Chirality : 0.042 0.228 3769 Planarity : 0.005 0.056 4428 Dihedral : 4.604 38.358 3385 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.30 % Favored : 93.50 % Rotamer: Outliers : 3.82 % Allowed : 24.35 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 3077 helix: 1.49 (0.14), residues: 1520 sheet: 0.54 (0.34), residues: 223 loop : -2.33 (0.15), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 55 HIS 0.004 0.001 HIS F 47 PHE 0.028 0.001 PHE I 116 TYR 0.024 0.001 TYR A 48 ARG 0.007 0.000 ARG F 260 Details of bonding type rmsd hydrogen bonds : bond 0.06538 ( 1146) hydrogen bonds : angle 4.05554 ( 3258) covalent geometry : bond 0.00355 (25504) covalent geometry : angle 0.63462 (34404) ********************** 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 765 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 660 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 321 TYR cc_start: 0.8802 (p90) cc_final: 0.8392 (p90) REVERT: E 512 ARG cc_start: 0.8301 (mtp85) cc_final: 0.8059 (mtp85) REVERT: E 544 GLU cc_start: 0.8125 (tt0) cc_final: 0.7808 (tt0) REVERT: E 549 LEU cc_start: 0.8452 (mp) cc_final: 0.8211 (mp) REVERT: E 594 SER cc_start: 0.8660 (t) cc_final: 0.8411 (m) REVERT: E 623 GLU cc_start: 0.7957 (tp30) cc_final: 0.7565 (tt0) REVERT: E 691 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7926 (mt-10) REVERT: F 104 GLU cc_start: 0.7586 (mp0) cc_final: 0.7187 (mp0) REVERT: F 117 THR cc_start: 0.8467 (t) cc_final: 0.8186 (m) REVERT: F 120 ASP cc_start: 0.7458 (p0) cc_final: 0.7190 (p0) REVERT: F 132 THR cc_start: 0.8859 (m) cc_final: 0.8413 (p) REVERT: F 155 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8528 (mt) REVERT: F 179 MET cc_start: 0.5204 (ppp) cc_final: 0.4677 (ptm) REVERT: F 288 LYS cc_start: 0.8480 (tttm) cc_final: 0.8178 (ttmm) REVERT: F 376 ILE cc_start: 0.8031 (mm) cc_final: 0.7592 (mp) REVERT: F 398 ASP cc_start: 0.8235 (p0) cc_final: 0.7898 (p0) REVERT: F 411 MET cc_start: 0.4753 (tmm) cc_final: 0.4331 (ppp) REVERT: F 442 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8176 (tt0) REVERT: F 457 GLU cc_start: 0.7940 (mp0) cc_final: 0.7642 (mp0) REVERT: F 475 ILE cc_start: 0.8188 (pt) cc_final: 0.7763 (mt) REVERT: F 571 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7422 (ttp80) REVERT: F 614 GLU cc_start: 0.7988 (pp20) cc_final: 0.7727 (pp20) REVERT: G 100 ASN cc_start: 0.8797 (m-40) cc_final: 0.8587 (m110) REVERT: A 18 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: A 34 LYS cc_start: 0.7597 (mtpp) cc_final: 0.7188 (mttm) REVERT: A 95 CYS cc_start: 0.7209 (p) cc_final: 0.7008 (t) REVERT: A 101 GLU cc_start: 0.7173 (mp0) cc_final: 0.6765 (mp0) REVERT: A 104 LYS cc_start: 0.7180 (ttmt) cc_final: 0.6971 (ttmt) REVERT: A 113 LYS cc_start: 0.8628 (tttm) cc_final: 0.8372 (ttpp) REVERT: A 114 GLU cc_start: 0.8121 (tp30) cc_final: 0.7533 (tp30) REVERT: A 117 PHE cc_start: 0.7727 (m-10) cc_final: 0.7171 (m-80) REVERT: A 122 VAL cc_start: 0.8948 (OUTLIER) cc_final: 0.8556 (t) REVERT: A 126 GLU cc_start: 0.7388 (pp20) cc_final: 0.7184 (pp20) REVERT: A 128 HIS cc_start: 0.7443 (m-70) cc_final: 0.7173 (m-70) REVERT: A 133 GLU cc_start: 0.7861 (mp0) cc_final: 0.7529 (mm-30) REVERT: A 153 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7694 (mm-30) REVERT: A 170 ARG cc_start: 0.8353 (mmm-85) cc_final: 0.8007 (mtm-85) REVERT: A 272 ASP cc_start: 0.8147 (p0) cc_final: 0.7892 (p0) REVERT: A 327 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6791 (pm20) REVERT: A 372 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6733 (tp30) REVERT: A 374 MET cc_start: 0.7177 (mpp) cc_final: 0.6951 (mpp) REVERT: A 469 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8692 (tt) REVERT: A 508 ARG cc_start: 0.7941 (mtt-85) cc_final: 0.7591 (mtt-85) REVERT: A 548 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8122 (ttm) REVERT: A 549 LEU cc_start: 0.8697 (mp) cc_final: 0.8450 (mm) REVERT: A 691 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7926 (mt-10) REVERT: A 712 THR cc_start: 0.8555 (t) cc_final: 0.8270 (m) REVERT: B 96 GLU cc_start: 0.8406 (tp30) cc_final: 0.8080 (tp30) REVERT: B 177 GLU cc_start: 0.8059 (tp30) cc_final: 0.7635 (tp30) REVERT: B 178 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8035 (tt0) REVERT: B 212 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8315 (m) REVERT: B 260 ARG cc_start: 0.8651 (ttt90) cc_final: 0.8349 (ttt90) REVERT: B 287 ARG cc_start: 0.8505 (tmm-80) cc_final: 0.8140 (ttm-80) REVERT: B 362 MET cc_start: 0.8427 (mpm) cc_final: 0.8146 (mpt) REVERT: B 481 LYS cc_start: 0.8588 (mtmm) cc_final: 0.8254 (mtmm) REVERT: B 584 ARG cc_start: 0.8183 (ttm-80) cc_final: 0.7957 (ttm-80) REVERT: B 667 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8618 (mt) REVERT: B 709 VAL cc_start: 0.8870 (t) cc_final: 0.8634 (m) REVERT: B 751 GLU cc_start: 0.7961 (tt0) cc_final: 0.7757 (tt0) REVERT: C 2 GLU cc_start: 0.7650 (mp0) cc_final: 0.7386 (mp0) REVERT: C 22 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8107 (mttt) REVERT: C 46 ARG cc_start: 0.8249 (ttp-170) cc_final: 0.8016 (ttp-170) REVERT: C 158 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7223 (pm20) REVERT: C 171 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: C 176 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7703 (tt) REVERT: C 177 LEU cc_start: 0.8462 (tt) cc_final: 0.8181 (tp) REVERT: C 187 LYS cc_start: 0.8141 (ttpp) cc_final: 0.7853 (ttpp) REVERT: C 188 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: C 756 MET cc_start: 0.4181 (mpm) cc_final: 0.3324 (mpm) REVERT: I 40 LEU cc_start: 0.7557 (mt) cc_final: 0.7342 (mm) REVERT: I 50 MET cc_start: 0.8050 (ppp) cc_final: 0.7294 (ppp) REVERT: I 68 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6473 (mp10) REVERT: I 74 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7572 (mm-30) REVERT: I 81 GLU cc_start: 0.7837 (mp0) cc_final: 0.7469 (mp0) REVERT: I 100 MET cc_start: 0.7217 (mmp) cc_final: 0.6791 (mmp) REVERT: I 113 ILE cc_start: 0.8659 (mt) cc_final: 0.8375 (mp) outliers start: 105 outliers final: 77 residues processed: 704 average time/residue: 1.6713 time to fit residues: 1317.7818 Evaluate side-chains 751 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 654 time to evaluate : 2.605 ------------------------------------------------------------------------------- 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 431 ASP Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 570 THR Chi-restraints excluded: chain E residue 597 GLU Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 618 THR 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 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 124 GLN Chi-restraints excluded: chain F residue 148 GLU Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 246 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 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 145 ILE Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 312 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 372 GLU Chi-restraints excluded: chain A residue 386 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 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 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 112 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 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 473 VAL 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 122 VAL Chi-restraints excluded: chain C residue 129 THR 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 213 ARG Chi-restraints excluded: chain C residue 723 ASN Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain J residue 10 GLN Chi-restraints excluded: chain J residue 29 ASN Chi-restraints excluded: chain J residue 31 MET 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 103 LEU Chi-restraints excluded: chain J residue 105 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 157 optimal weight: 0.0670 chunk 281 optimal weight: 4.9990 chunk 266 optimal weight: 0.7980 chunk 180 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 255 optimal weight: 0.9980 chunk 277 optimal weight: 0.7980 chunk 250 optimal weight: 0.9990 chunk 89 optimal weight: 0.4980 chunk 138 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 328 ASN A 92 ASN A 136 ASN A 654 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.120871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.098453 restraints weight = 37452.210| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.05 r_work: 0.3068 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25504 Z= 0.173 Angle : 0.656 10.993 34404 Z= 0.343 Chirality : 0.043 0.203 3769 Planarity : 0.005 0.055 4428 Dihedral : 4.650 38.329 3385 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.30 % Favored : 93.50 % Rotamer: Outliers : 4.03 % Allowed : 24.09 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 3077 helix: 1.47 (0.14), residues: 1518 sheet: 0.53 (0.34), residues: 231 loop : -2.35 (0.15), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 55 HIS 0.004 0.001 HIS F 47 PHE 0.030 0.002 PHE B 512 TYR 0.021 0.001 TYR A 48 ARG 0.008 0.000 ARG F 260 Details of bonding type rmsd hydrogen bonds : bond 0.06993 ( 1146) hydrogen bonds : angle 4.09165 ( 3258) covalent geometry : bond 0.00404 (25504) covalent geometry : angle 0.65595 (34404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26183.63 seconds wall clock time: 450 minutes 50.26 seconds (27050.26 seconds total)