Starting phenix.real_space_refine on Thu Sep 18 19:35:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xew_38297/09_2025/8xew_38297.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xew_38297/09_2025/8xew_38297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xew_38297/09_2025/8xew_38297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xew_38297/09_2025/8xew_38297.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xew_38297/09_2025/8xew_38297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xew_38297/09_2025/8xew_38297.map" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 12798 2.51 5 N 3202 2.21 5 O 3562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19631 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2182 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 10, 'TRANS': 265} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2111 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 10, 'TRANS': 265} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 12, 'ASN:plan1': 6, 'GLU:plan': 10, 'GLN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 112 Chain: "C" Number of atoms: 7799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7799 Classifications: {'peptide': 994} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PTRANS': 19, 'TRANS': 974} Unresolved non-hydrogen bonds: 481 Unresolved non-hydrogen angles: 575 Unresolved non-hydrogen dihedrals: 403 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 37, 'ASP:plan': 19, 'ASN:plan1': 6, 'ARG:plan': 8, 'GLN:plan1': 3, 'PHE:plan': 4, 'HIS:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 318 Chain: "D" Number of atoms: 7539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7539 Classifications: {'peptide': 984} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 172} Link IDs: {'PTRANS': 19, 'TRANS': 964} Unresolved non-hydrogen bonds: 656 Unresolved non-hydrogen angles: 787 Unresolved non-hydrogen dihedrals: 533 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 25, 'ASN:plan1': 18, 'GLU:plan': 53, 'GLN:plan1': 8, 'ARG:plan': 9, 'PHE:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 441 Time building chain proxies: 4.53, per 1000 atoms: 0.23 Number of scatterers: 19631 At special positions: 0 Unit cell: (99.45, 126.75, 184.6, 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 69 16.00 O 3562 8.00 N 3202 7.00 C 12798 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 966.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4806 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 6 sheets defined 62.5% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 23 through 39 removed outlier: 3.788A pdb=" N GLU A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.625A pdb=" N THR A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 70 removed outlier: 4.021A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 95 removed outlier: 3.650A pdb=" N ILE A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Proline residue: A 88 - end of helix removed outlier: 3.702A pdb=" N PHE A 91 " --> pdb=" O ILE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 109 removed outlier: 3.555A pdb=" N ILE A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A 109 " --> pdb=" O LYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 123 removed outlier: 4.080A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 removed outlier: 3.611A pdb=" N ARG A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 197 through 210 removed outlier: 4.057A pdb=" N LYS A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 235 removed outlier: 3.515A pdb=" N LEU A 228 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 262 removed outlier: 3.638A pdb=" N TYR A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 261 " --> pdb=" O THR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.836A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 40 removed outlier: 3.827A pdb=" N LYS B 31 " --> pdb=" O VAL B 27 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 33 " --> pdb=" O CYS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.583A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 55 No H-bonds generated for 'chain 'B' and resid 53 through 55' Processing helix chain 'B' and resid 58 through 71 removed outlier: 4.203A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 86 removed outlier: 3.944A pdb=" N LEU B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 81 through 86' Processing helix chain 'B' and resid 86 through 95 Processing helix chain 'B' and resid 97 through 109 removed outlier: 3.594A pdb=" N ILE B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 104 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.791A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 137 through 146 removed outlier: 4.759A pdb=" N TRP B 143 " --> pdb=" O ASP B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.525A pdb=" N ASP B 157 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL B 158 " --> pdb=" O GLU B 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 154 through 158' Processing helix chain 'B' and resid 187 through 192 Processing helix chain 'B' and resid 197 through 211 removed outlier: 3.520A pdb=" N LYS B 205 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 235 removed outlier: 3.557A pdb=" N MET B 227 " --> pdb=" O TYR B 223 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU B 228 " --> pdb=" O ASN B 224 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.524A pdb=" N ILE B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 296 removed outlier: 3.542A pdb=" N SER B 287 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 289 " --> pdb=" O ARG B 285 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 20 removed outlier: 3.601A pdb=" N GLU C 17 " --> pdb=" O GLU C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 40 removed outlier: 3.522A pdb=" N VAL C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 53 removed outlier: 3.672A pdb=" N LEU C 53 " --> pdb=" O GLY C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 71 removed outlier: 3.633A pdb=" N LEU C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 65 " --> pdb=" O ARG C 61 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU C 68 " --> pdb=" O ASP C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 96 removed outlier: 3.611A pdb=" N LEU C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG C 86 " --> pdb=" O ASP C 82 " (cutoff:3.500A) Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 99 through 108 Processing helix chain 'C' and resid 115 through 123 removed outlier: 3.946A pdb=" N ASP C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 145 removed outlier: 3.597A pdb=" N ALA C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP C 143 " --> pdb=" O ASP C 139 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 197 through 211 removed outlier: 3.635A pdb=" N SER C 201 " --> pdb=" O TYR C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 235 removed outlier: 3.881A pdb=" N TRP C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS C 234 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 235 " --> pdb=" O TRP C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 264 Processing helix chain 'C' and resid 281 through 298 removed outlier: 3.676A pdb=" N VAL C 289 " --> pdb=" O ARG C 285 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 317 removed outlier: 3.578A pdb=" N ILE C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY C 314 " --> pdb=" O ASP C 310 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS C 315 " --> pdb=" O TYR C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 321 Processing helix chain 'C' and resid 329 through 334 removed outlier: 3.593A pdb=" N PHE C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 366 removed outlier: 3.674A pdb=" N GLU C 365 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER C 366 " --> pdb=" O GLU C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'C' and resid 378 through 392 removed outlier: 4.079A pdb=" N LYS C 390 " --> pdb=" O ASN C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 400 No H-bonds generated for 'chain 'C' and resid 398 through 400' Processing helix chain 'C' and resid 411 through 416 Processing helix chain 'C' and resid 417 through 427 Processing helix chain 'C' and resid 432 through 445 removed outlier: 3.560A pdb=" N LYS C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 464 removed outlier: 3.794A pdb=" N ASP C 453 " --> pdb=" O GLU C 449 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN C 461 " --> pdb=" O ASN C 457 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE C 463 " --> pdb=" O ILE C 459 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 487 removed outlier: 3.656A pdb=" N TYR C 471 " --> pdb=" O ASN C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 494 removed outlier: 3.514A pdb=" N GLY C 494 " --> pdb=" O THR C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 500 removed outlier: 3.855A pdb=" N PHE C 500 " --> pdb=" O GLY C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 519 removed outlier: 3.736A pdb=" N GLU C 516 " --> pdb=" O LEU C 512 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG C 517 " --> pdb=" O ALA C 513 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU C 518 " --> pdb=" O ARG C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 531 removed outlier: 3.689A pdb=" N ASP C 526 " --> pdb=" O ASN C 523 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N PHE C 528 " --> pdb=" O ASP C 525 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN C 529 " --> pdb=" O ASP C 526 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET C 531 " --> pdb=" O PHE C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 540 through 547 removed outlier: 4.567A pdb=" N PHE C 544 " --> pdb=" O ILE C 541 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 545 " --> pdb=" O LEU C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 557 Processing helix chain 'C' and resid 561 through 564 Processing helix chain 'C' and resid 565 through 570 removed outlier: 3.519A pdb=" N SER C 570 " --> pdb=" O ARG C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 598 removed outlier: 3.517A pdb=" N ASN C 591 " --> pdb=" O ARG C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 604 Processing helix chain 'C' and resid 605 through 634 removed outlier: 3.585A pdb=" N ASP C 632 " --> pdb=" O THR C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 659 Processing helix chain 'C' and resid 660 through 671 removed outlier: 3.589A pdb=" N ASN C 666 " --> pdb=" O ASP C 662 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 667 " --> pdb=" O ASP C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 676 Processing helix chain 'C' and resid 680 through 700 removed outlier: 4.122A pdb=" N GLU C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR C 687 " --> pdb=" O LYS C 683 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN C 698 " --> pdb=" O GLU C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 722 removed outlier: 3.904A pdb=" N GLN C 711 " --> pdb=" O VAL C 707 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE C 713 " --> pdb=" O TYR C 709 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER C 714 " --> pdb=" O THR C 710 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU C 715 " --> pdb=" O GLN C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 726 removed outlier: 3.632A pdb=" N VAL C 726 " --> pdb=" O ALA C 723 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 723 through 726' Processing helix chain 'C' and resid 730 through 742 removed outlier: 4.119A pdb=" N LYS C 735 " --> pdb=" O GLU C 731 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE C 736 " --> pdb=" O GLY C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 761 removed outlier: 3.548A pdb=" N VAL C 756 " --> pdb=" O GLY C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 784 removed outlier: 3.835A pdb=" N ILE C 774 " --> pdb=" O SER C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 800 through 812 removed outlier: 4.089A pdb=" N TYR C 804 " --> pdb=" O TYR C 800 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY C 805 " --> pdb=" O SER C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 834 through 839 Processing helix chain 'C' and resid 841 through 845 removed outlier: 3.504A pdb=" N LEU C 844 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 855 removed outlier: 3.684A pdb=" N SER C 855 " --> pdb=" O SER C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 871 Processing helix chain 'C' and resid 878 through 903 removed outlier: 3.698A pdb=" N LEU C 884 " --> pdb=" O GLU C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 922 removed outlier: 3.516A pdb=" N ILE C 918 " --> pdb=" O SER C 914 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP C 919 " --> pdb=" O THR C 915 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR C 920 " --> pdb=" O PHE C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 934 removed outlier: 3.873A pdb=" N MET C 930 " --> pdb=" O ASN C 927 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU C 931 " --> pdb=" O SER C 928 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU C 932 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 934 " --> pdb=" O GLU C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 945 removed outlier: 3.864A pdb=" N VAL C 944 " --> pdb=" O TYR C 940 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 945 " --> pdb=" O ASP C 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 940 through 945' Processing helix chain 'C' and resid 950 through 954 Processing helix chain 'C' and resid 955 through 962 removed outlier: 3.560A pdb=" N TRP C 958 " --> pdb=" O ILE C 955 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C 959 " --> pdb=" O PRO C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 970 Processing helix chain 'C' and resid 971 through 973 No H-bonds generated for 'chain 'C' and resid 971 through 973' Processing helix chain 'C' and resid 976 through 989 removed outlier: 3.965A pdb=" N ILE C 981 " --> pdb=" O LYS C 977 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU C 982 " --> pdb=" O HIS C 978 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG C 987 " --> pdb=" O VAL C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1002 removed outlier: 3.660A pdb=" N ILE C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C1000 " --> pdb=" O TYR C 996 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 38 removed outlier: 3.697A pdb=" N LYS D 31 " --> pdb=" O VAL D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 53 removed outlier: 4.016A pdb=" N SER D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 53 " --> pdb=" O GLY D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 72 removed outlier: 3.963A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 95 removed outlier: 3.622A pdb=" N TYR D 84 " --> pdb=" O SER D 80 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG D 86 " --> pdb=" O ASP D 82 " (cutoff:3.500A) Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 96 through 109 removed outlier: 3.525A pdb=" N ASP D 101 " --> pdb=" O GLU D 97 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY D 102 " --> pdb=" O MET D 98 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE D 103 " --> pdb=" O ALA D 99 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 104 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 122 Processing helix chain 'D' and resid 123 through 125 No H-bonds generated for 'chain 'D' and resid 123 through 125' Processing helix chain 'D' and resid 136 through 146 removed outlier: 3.520A pdb=" N CYS D 142 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TRP D 143 " --> pdb=" O ASP D 139 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS D 144 " --> pdb=" O THR D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 158 removed outlier: 3.618A pdb=" N VAL D 158 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.726A pdb=" N SER D 201 " --> pdb=" O TYR D 197 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS D 205 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.856A pdb=" N LEU D 228 " --> pdb=" O ASN D 224 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TRP D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 263 Processing helix chain 'D' and resid 281 through 295 removed outlier: 3.698A pdb=" N VAL D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 313 removed outlier: 3.703A pdb=" N VAL D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE D 309 " --> pdb=" O ASP D 305 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 321 removed outlier: 3.844A pdb=" N PHE D 320 " --> pdb=" O SER D 317 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA D 321 " --> pdb=" O PRO D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 363 removed outlier: 3.611A pdb=" N ARG D 359 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE D 361 " --> pdb=" O MET D 357 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU D 362 " --> pdb=" O GLU D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 392 removed outlier: 3.553A pdb=" N LEU D 384 " --> pdb=" O ARG D 380 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN D 386 " --> pdb=" O ASN D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 removed outlier: 3.510A pdb=" N HIS D 415 " --> pdb=" O SER D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 426 Processing helix chain 'D' and resid 431 through 445 removed outlier: 3.708A pdb=" N LYS D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 462 Processing helix chain 'D' and resid 467 through 490 removed outlier: 4.598A pdb=" N TYR D 471 " --> pdb=" O ASN D 467 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D 473 " --> pdb=" O CYS D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 520 removed outlier: 4.517A pdb=" N ARG D 517 " --> pdb=" O ALA D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.714A pdb=" N LEU D 527 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 550 removed outlier: 3.961A pdb=" N PHE D 544 " --> pdb=" O ILE D 541 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER D 546 " --> pdb=" O GLU D 543 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP D 547 " --> pdb=" O PHE D 544 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASN D 548 " --> pdb=" O LEU D 545 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLN D 549 " --> pdb=" O SER D 546 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHE D 550 " --> pdb=" O ASP D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 572 removed outlier: 3.590A pdb=" N LYS D 557 " --> pdb=" O ASP D 553 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN D 563 " --> pdb=" O PHE D 559 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER D 570 " --> pdb=" O ARG D 566 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY D 572 " --> pdb=" O GLU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 598 removed outlier: 3.788A pdb=" N VAL D 583 " --> pdb=" O SER D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 605 removed outlier: 3.530A pdb=" N VAL D 603 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 628 removed outlier: 3.527A pdb=" N LEU D 618 " --> pdb=" O ASN D 614 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D 619 " --> pdb=" O SER D 615 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR D 625 " --> pdb=" O GLU D 621 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR D 628 " --> pdb=" O GLU D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 640 removed outlier: 3.969A pdb=" N SER D 637 " --> pdb=" O GLU D 633 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY D 640 " --> pdb=" O PHE D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 659 Processing helix chain 'D' and resid 660 through 671 removed outlier: 3.709A pdb=" N LEU D 667 " --> pdb=" O ASP D 663 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ARG D 669 " --> pdb=" O LYS D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 676 Processing helix chain 'D' and resid 682 through 700 removed outlier: 3.601A pdb=" N THR D 696 " --> pdb=" O ALA D 692 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS D 697 " --> pdb=" O GLU D 693 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN D 698 " --> pdb=" O GLU D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 722 removed outlier: 3.847A pdb=" N GLN D 711 " --> pdb=" O VAL D 707 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE D 713 " --> pdb=" O TYR D 709 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER D 714 " --> pdb=" O THR D 710 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 720 " --> pdb=" O ALA D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 742 removed outlier: 4.465A pdb=" N LYS D 735 " --> pdb=" O GLU D 731 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE D 736 " --> pdb=" O GLY D 732 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE D 742 " --> pdb=" O LYS D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 751 through 761 removed outlier: 4.006A pdb=" N TYR D 755 " --> pdb=" O ILE D 751 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL D 756 " --> pdb=" O GLY D 752 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TRP D 757 " --> pdb=" O LYS D 753 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG D 760 " --> pdb=" O VAL D 756 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 783 removed outlier: 3.579A pdb=" N VAL D 780 " --> pdb=" O ASP D 776 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 781 " --> pdb=" O ASP D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 802 through 812 removed outlier: 4.052A pdb=" N PHE D 811 " --> pdb=" O LEU D 807 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 824 removed outlier: 3.552A pdb=" N THR D 824 " --> pdb=" O LEU D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 832 through 840 removed outlier: 4.295A pdb=" N ASP D 836 " --> pdb=" O GLN D 832 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE D 837 " --> pdb=" O LYS D 833 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU D 838 " --> pdb=" O GLN D 834 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE D 839 " --> pdb=" O ILE D 835 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS D 840 " --> pdb=" O ASP D 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 832 through 840' Processing helix chain 'D' and resid 841 through 845 Processing helix chain 'D' and resid 846 through 857 removed outlier: 3.603A pdb=" N HIS D 852 " --> pdb=" O ASN D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 861 through 872 removed outlier: 3.752A pdb=" N ARG D 870 " --> pdb=" O MET D 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 903 removed outlier: 3.568A pdb=" N GLU D 882 " --> pdb=" O THR D 878 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE D 886 " --> pdb=" O GLU D 882 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE D 897 " --> pdb=" O LYS D 893 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL D 898 " --> pdb=" O VAL D 894 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU D 901 " --> pdb=" O ILE D 897 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS D 902 " --> pdb=" O VAL D 898 " (cutoff:3.500A) Processing helix chain 'D' and resid 911 through 922 Processing helix chain 'D' and resid 937 through 945 Processing helix chain 'D' and resid 950 through 954 Processing helix chain 'D' and resid 955 through 962 removed outlier: 3.537A pdb=" N LEU D 959 " --> pdb=" O PRO D 956 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR D 962 " --> pdb=" O LEU D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 963 through 971 removed outlier: 3.587A pdb=" N LEU D 967 " --> pdb=" O ASN D 963 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D 969 " --> pdb=" O LYS D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 989 removed outlier: 3.578A pdb=" N VAL D 980 " --> pdb=" O MET D 976 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE D 981 " --> pdb=" O LYS D 977 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLU D 982 " --> pdb=" O HIS D 978 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL D 983 " --> pdb=" O HIS D 979 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS D 989 " --> pdb=" O LYS D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1004 removed outlier: 3.590A pdb=" N GLU D 998 " --> pdb=" O LYS D 994 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR D1003 " --> pdb=" O ILE D 999 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 5.726A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU A 42 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N ILE A 130 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE A 44 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 152 removed outlier: 3.874A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE B 44 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.357A pdb=" N SER C 150 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LYS C 169 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE C 152 " --> pdb=" O LYS C 169 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS C 128 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE C 44 " --> pdb=" O HIS C 128 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE C 213 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE C 246 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N PHE C 215 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N PHE C 245 " --> pdb=" O ILE C 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 338 through 340 Processing sheet with id=AA5, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.500A pdb=" N SER D 150 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS D 169 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE D 152 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU D 42 " --> pdb=" O HIS D 128 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE D 130 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N PHE D 44 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE D 213 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE D 246 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE D 215 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE D 245 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 338 through 340 836 hydrogen bonds defined for protein. 2397 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: 3.17 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3142 1.31 - 1.44: 5838 1.44 - 1.56: 11015 1.56 - 1.69: 2 1.69 - 1.81: 114 Bond restraints: 20111 Sorted by residual: bond pdb=" C PRO C 113 " pdb=" O PRO C 113 " ideal model delta sigma weight residual 1.232 1.184 0.048 1.20e-02 6.94e+03 1.62e+01 bond pdb=" C ARG B 86 " pdb=" O ARG B 86 " ideal model delta sigma weight residual 1.235 1.187 0.048 1.25e-02 6.40e+03 1.45e+01 bond pdb=" CA SER C 54 " pdb=" CB SER C 54 " ideal model delta sigma weight residual 1.536 1.477 0.059 1.58e-02 4.01e+03 1.41e+01 bond pdb=" CA HIS A 67 " pdb=" C HIS A 67 " ideal model delta sigma weight residual 1.522 1.568 -0.046 1.43e-02 4.89e+03 1.04e+01 bond pdb=" N MET C 124 " pdb=" CA MET C 124 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.32e-02 5.74e+03 1.01e+01 ... (remaining 20106 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 26040 1.90 - 3.80: 1104 3.80 - 5.69: 143 5.69 - 7.59: 33 7.59 - 9.49: 8 Bond angle restraints: 27328 Sorted by residual: angle pdb=" N LYS D 538 " pdb=" CA LYS D 538 " pdb=" C LYS D 538 " ideal model delta sigma weight residual 114.56 107.05 7.51 1.27e+00 6.20e-01 3.49e+01 angle pdb=" N MET C 124 " pdb=" CA MET C 124 " pdb=" C MET C 124 " ideal model delta sigma weight residual 113.02 106.29 6.73 1.20e+00 6.94e-01 3.15e+01 angle pdb=" N THR B 132 " pdb=" CA THR B 132 " pdb=" C THR B 132 " ideal model delta sigma weight residual 112.88 106.08 6.80 1.29e+00 6.01e-01 2.78e+01 angle pdb=" N GLU C 369 " pdb=" CA GLU C 369 " pdb=" C GLU C 369 " ideal model delta sigma weight residual 111.71 106.01 5.70 1.15e+00 7.56e-01 2.45e+01 angle pdb=" N ILE D 316 " pdb=" CA ILE D 316 " pdb=" C ILE D 316 " ideal model delta sigma weight residual 113.71 109.13 4.58 9.50e-01 1.11e+00 2.33e+01 ... (remaining 27323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.85: 11064 14.85 - 29.70: 541 29.70 - 44.55: 103 44.55 - 59.40: 18 59.40 - 74.25: 8 Dihedral angle restraints: 11734 sinusoidal: 4240 harmonic: 7494 Sorted by residual: dihedral pdb=" CA PHE C 699 " pdb=" C PHE C 699 " pdb=" N SER C 700 " pdb=" CA SER C 700 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA GLU C 298 " pdb=" C GLU C 298 " pdb=" N ASN C 299 " pdb=" CA ASN C 299 " ideal model delta harmonic sigma weight residual -180.00 -152.23 -27.77 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA GLU D 298 " pdb=" C GLU D 298 " pdb=" N ASN D 299 " pdb=" CA ASN D 299 " ideal model delta harmonic sigma weight residual -180.00 -153.77 -26.23 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 11731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2077 0.052 - 0.103: 827 0.103 - 0.155: 140 0.155 - 0.207: 12 0.207 - 0.258: 4 Chirality restraints: 3060 Sorted by residual: chirality pdb=" CB VAL C 603 " pdb=" CA VAL C 603 " pdb=" CG1 VAL C 603 " pdb=" CG2 VAL C 603 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE D 216 " pdb=" CA ILE D 216 " pdb=" CG1 ILE D 216 " pdb=" CG2 ILE D 216 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB THR C 405 " pdb=" CA THR C 405 " pdb=" OG1 THR C 405 " pdb=" CG2 THR C 405 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 3057 not shown) Planarity restraints: 3463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 124 " 0.020 2.00e-02 2.50e+03 4.21e-02 1.78e+01 pdb=" C MET C 124 " -0.073 2.00e-02 2.50e+03 pdb=" O MET C 124 " 0.027 2.00e-02 2.50e+03 pdb=" N ASN C 125 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 624 " -0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C GLU C 624 " 0.068 2.00e-02 2.50e+03 pdb=" O GLU C 624 " -0.025 2.00e-02 2.50e+03 pdb=" N TYR C 625 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 64 " -0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C ASP C 64 " 0.064 2.00e-02 2.50e+03 pdb=" O ASP C 64 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS C 65 " -0.022 2.00e-02 2.50e+03 ... (remaining 3460 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 6210 2.82 - 3.34: 17296 3.34 - 3.86: 31665 3.86 - 4.38: 38018 4.38 - 4.90: 63802 Nonbonded interactions: 156991 Sorted by model distance: nonbonded pdb=" OG SER D 579 " pdb=" OD1 ASP D 581 " model vdw 2.295 3.040 nonbonded pdb=" O ARG D 987 " pdb=" OG SER D 991 " model vdw 2.298 3.040 nonbonded pdb=" O GLU C 516 " pdb=" OG1 THR C 520 " model vdw 2.313 3.040 nonbonded pdb=" O GLU D 362 " pdb=" OG SER D 366 " model vdw 2.314 3.040 nonbonded pdb=" OD1 ASN A 115 " pdb=" ND1 HIS A 118 " model vdw 2.320 3.120 ... (remaining 156986 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 or (resid 23 through 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 27 or (resid 28 and (name N or nam \ e CA or name C or name O or name CB )) or resid 29 through 30 or (resid 31 throu \ gh 32 and (name N or name CA or name C or name O or name CB )) or resid 33 throu \ gh 34 or (resid 35 and (name N or name CA or name C or name O or name CB )) or r \ esid 36 through 54 or (resid 55 and (name N or name CA or name C or name O or na \ me CB )) or resid 56 through 57 or (resid 58 and (name N or name CA or name C or \ name O or name CB )) or resid 59 through 60 or (resid 61 and (name N or name CA \ or name C or name O or name CB )) or resid 62 through 69 or (resid 70 and (name \ N or name CA or name C or name O or name CB )) or resid 71 through 85 or (resid \ 86 and (name N or name CA or name C or name O or name CB )) or resid 87 through \ 105 or (resid 106 and (name N or name CA or name C or name O or name CB )) or r \ esid 107 through 118 or (resid 119 and (name N or name CA or name C or name O or \ name CB )) or resid 120 through 124 or (resid 125 and (name N or name CA or nam \ e C or name O or name CB )) or resid 126 through 138 or (resid 139 and (name N o \ r name CA or name C or name O or name CB )) or resid 140 through 143 or (resid 1 \ 44 and (name N or name CA or name C or name O or name CB )) or resid 145 through \ 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) or r \ esid 148 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 194 or (resid 195 and (name N or name CA or nam \ e C or name O or name CB )) or resid 196 through 253 or (resid 254 through 256 a \ nd (name N or name CA or name C or name O or name CB )) or resid 257 through 261 \ or (resid 262 through 263 and (name N or name CA or name C or name O or name CB \ )) or resid 264 through 277 or (resid 278 through 279 and (name N or name CA or \ name C or name O or name CB )) or resid 280 through 297)) selection = (chain 'B' and (resid 22 through 53 or (resid 54 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 82 or (resid 83 and (na \ me N or name CA or name C or name O or name CB )) or resid 84 through 94 or (res \ id 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throu \ gh 159 or (resid 160 through 161 and (name N or name CA or name C or name O or n \ ame CB )) or resid 162 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB )) or resid 177 through 178 or (resid 179 and (name N or \ name CA or name C or name O or name CB )) or resid 180 or (resid 181 and (name N \ or name CA or name C or name O or name CB )) or resid 182 through 297)) } ncs_group { reference = (chain 'C' and (resid 22 or (resid 23 through 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 27 or (resid 28 and (name N or nam \ e CA or name C or name O or name CB )) or resid 29 through 30 or (resid 31 throu \ gh 32 and (name N or name CA or name C or name O or name CB )) or resid 33 throu \ gh 34 or (resid 35 and (name N or name CA or name C or name O or name CB )) or r \ esid 36 through 57 or (resid 58 and (name N or name CA or name C or name O or na \ me CB )) or resid 59 through 60 or (resid 61 and (name N or name CA or name C or \ name O or name CB )) or resid 62 through 69 or (resid 70 and (name N or name CA \ or name C or name O or name CB )) or resid 71 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB )) or (resid 96 through 99 and (nam \ e N or name CA or name C or name O or name CB )) or resid 100 through 105 or (re \ sid 106 and (name N or name CA or name C or name O or name CB )) or resid 107 th \ rough 118 or (resid 119 through 120 and (name N or name CA or name C or name O o \ r name CB )) or resid 121 through 124 or (resid 125 and (name N or name CA or na \ me C or name O or name CB )) or resid 126 through 135 or (resid 136 and (name N \ or name CA or name C or name O or name CB )) or resid 137 through 143 or (resid \ 144 and (name N or name CA or name C or name O or name CB )) or resid 145 throug \ h 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) or \ resid 148 through 187 or (resid 188 and (name N or name CA or name C or name O o \ r name CB )) or resid 189 through 193 or (resid 194 and (name N or name CA or na \ me C or name O or name CB )) or resid 195 through 225 or (resid 226 through 227 \ and (name N or name CA or name C or name O or name CB )) or resid 228 through 22 \ 9 or (resid 230 and (name N or name CA or name C or name O or name CB )) or resi \ d 231 through 232 or (resid 233 and (name N or name CA or name C or name O or na \ me CB )) or resid 234 through 237 or (resid 238 and (name N or name CA or name C \ or name O or name CB )) or resid 239 through 254 or (resid 255 and (name N or n \ ame CA or name C or name O or name CB )) or resid 256 through 258 or (resid 259 \ and (name N or name CA or name C or name O or name CB )) or resid 260 through 26 \ 1 or (resid 262 through 263 and (name N or name CA or name C or name O or name C \ B )) or resid 264 through 277 or (resid 278 through 279 and (name N or name CA o \ r name C or name O or name CB )) or resid 280 through 290 or (resid 291 and (nam \ e N or name CA or name C or name O or name CB )) or resid 292 through 299 or (re \ sid 300 and (name N or name CA or name C or name O or name CB )) or resid 301 or \ (resid 302 and (name N or name CA or name C or name O or name CB )) or resid 30 \ 3 through 306 or (resid 307 and (name N or name CA or name C or name O or name C \ B )) or resid 308 through 330 or (resid 331 and (name N or name CA or name C or \ name O or name CB )) or resid 332 through 347 or (resid 348 and (name N or name \ CA or name C or name O or name CB )) or resid 349 through 375 or (resid 376 and \ (name N or name CA or name C or name O or name CB )) or resid 377 through 378 or \ (resid 379 and (name N or name CA or name C or name O or name CB )) or resid 38 \ 0 through 393 or (resid 394 and (name N or name CA or name C or name O or name C \ B )) or resid 395 through 397 or (resid 398 through 400 and (name N or name CA o \ r name C or name O or name CB )) or resid 401 through 402 or (resid 403 through \ 404 and (name N or name CA or name C or name O or name CB )) or resid 405 throug \ h 407 or (resid 408 and (name N or name CA or name C or name O or name CB )) or \ resid 409 through 422 or (resid 423 and (name N or name CA or name C or name O o \ r name CB )) or resid 424 through 432 or (resid 433 and (name N or name CA or na \ me C or name O or name CB )) or resid 434 through 448 or (resid 449 and (name N \ or name CA or name C or name O or name CB )) or resid 450 through 462 or (resid \ 463 through 465 and (name N or name CA or name C or name O or name CB )) or resi \ d 466 through 490 or (resid 491 and (name N or name CA or name C or name O or na \ me CB )) or resid 492 or (resid 493 and (name N or name CA or name C or name O o \ r name CB )) or resid 494 through 507 or (resid 508 through 510 and (name N or n \ ame CA or name C or name O or name CB )) or resid 511 through 515 or (resid 516 \ through 517 and (name N or name CA or name C or name O or name CB )) or resid 51 \ 8 through 519 or (resid 520 through 521 and (name N or name CA or name C or name \ O or name CB )) or resid 522 through 533 or (resid 534 and (name N or name CA o \ r name C or name O or name CB )) or resid 535 through 536 or (resid 537 through \ 538 and (name N or name CA or name C or name O or name CB )) or resid 539 or (re \ sid 540 and (name N or name CA or name C or name O or name CB )) or resid 541 th \ rough 542 or (resid 543 and (name N or name CA or name C or name O or name CB )) \ or resid 544 through 552 or (resid 553 and (name N or name CA or name C or name \ O or name CB )) or resid 554 through 559 or (resid 560 and (name N or name CA o \ r name C or name O or name CB )) or resid 561 through 606 or (resid 607 and (nam \ e N or name CA or name C or name O or name CB )) or resid 608 through 620 or (re \ sid 621 and (name N or name CA or name C or name O or name CB )) or resid 622 th \ rough 647 or (resid 648 and (name N or name CA or name C or name O or name CB )) \ or resid 649 through 679 or (resid 680 and (name N or name CA or name C or name \ O or name CB )) or resid 681 through 684 or (resid 685 through 686 and (name N \ or name CA or name C or name O or name CB )) or resid 687 through 692 or (resid \ 693 through 694 and (name N or name CA or name C or name O or name CB )) or resi \ d 695 through 696 or (resid 697 and (name N or name CA or name C or name O or na \ me CB )) or resid 698 or (resid 699 and (name N or name CA or name C or name O o \ r name CB )) or resid 700 through 710 or (resid 711 and (name N or name CA or na \ me C or name O or name CB )) or resid 712 through 737 or (resid 738 through 739 \ and (name N or name CA or name C or name O or name CB )) or resid 740 through 74 \ 5 or (resid 746 through 747 and (name N or name CA or name C or name O or name C \ B )) or resid 748 through 758 or (resid 759 and (name N or name CA or name C or \ name O or name CB )) or resid 760 through 765 or (resid 766 and (name N or name \ CA or name C or name O or name CB )) or resid 767 through 784 or (resid 785 and \ (name N or name CA or name C or name O or name CB )) or resid 786 through 788 or \ (resid 789 through 790 and (name N or name CA or name C or name O or name CB )) \ or resid 791 through 808 or (resid 809 and (name N or name CA or name C or name \ O or name CB )) or resid 810 through 811 or (resid 812 through 814 and (name N \ or name CA or name C or name O or name CB )) or resid 815 through 817 or (resid \ 818 through 819 and (name N or name CA or name C or name O or name CB )) or resi \ d 820 through 831 or (resid 832 through 833 and (name N or name CA or name C or \ name O or name CB )) or resid 834 through 835 or (resid 836 and (name N or name \ CA or name C or name O or name CB )) or resid 837 through 846 or (resid 847 thro \ ugh 850 and (name N or name CA or name C or name O or name CB )) or resid 851 th \ rough 857 or (resid 858 and (name N or name CA or name C or name O or name CB )) \ or resid 859 through 862 or (resid 863 through 864 and (name N or name CA or na \ me C or name O or name CB )) or resid 865 through 874 or (resid 875 through 876 \ and (name N or name CA or name C or name O or name CB )) or resid 877 through 89 \ 8 or (resid 899 through 902 and (name N or name CA or name C or name O or name C \ B )) or resid 903 through 923 or (resid 924 and (name N or name CA or name C or \ name O or name CB )) or resid 925 through 946 or (resid 947 through 948 and (nam \ e N or name CA or name C or name O or name CB )) or resid 949 through 964 or (re \ sid 965 and (name N or name CA or name C or name O or name CB )) or resid 966 th \ rough 1005)) selection = (chain 'D' and (resid 22 through 67 or (resid 68 through 70 and (name N or name \ CA or name C or name O or name CB )) or resid 71 through 81 or (resid 82 through \ 83 and (name N or name CA or name C or name O or name CB )) or resid 84 through \ 159 or (resid 160 through 161 and (name N or name CA or name C or name O or nam \ e CB )) or resid 162 through 175 or (resid 176 and (name N or name CA or name C \ or name O or name CB )) or resid 177 through 178 or (resid 179 and (name N or na \ me CA or name C or name O or name CB )) or resid 180 or (resid 181 and (name N o \ r name CA or name C or name O or name CB )) or resid 182 through 369 or (resid 3 \ 70 and (name N or name CA or name C or name O or name CB )) or resid 371 through \ 463 or (resid 464 through 465 and (name N or name CA or name C or name O or nam \ e CB )) or resid 466 through 503 or (resid 504 through 505 and (name N or name C \ A or name C or name O or name CB )) or resid 506 through 525 or (resid 526 and ( \ name N or name CA or name C or name O or name CB )) or resid 527 through 565 or \ (resid 566 and (name N or name CA or name C or name O or name CB )) or resid 567 \ through 568 or (resid 569 and (name N or name CA or name C or name O or name CB \ )) or resid 570 or (resid 571 and (name N or name CA or name C or name O or nam \ e CB )) or resid 572 through 577 or (resid 578 and (name N or name CA or name C \ or name O or name CB )) or resid 579 through 626 or (resid 627 and (name N or na \ me CA or name C or name O or name CB )) or resid 628 through 638 or (resid 639 a \ nd (name N or name CA or name C or name O or name CB )) or (resid 640 through 64 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 643 through \ 673 or (resid 674 through 675 and (name N or name CA or name C or name O or name \ CB )) or resid 676 through 873 or (resid 874 through 876 and (name N or name CA \ or name C or name O or name CB )) or resid 877 through 881 or (resid 882 throug \ h 884 and (name N or name CA or name C or name O or name CB )) or resid 885 thro \ ugh 889 or (resid 890 and (name N or name CA or name C or name O or name CB )) o \ r resid 891 or (resid 892 through 893 and (name N or name CA or name C or name O \ or name CB )) or resid 894 through 895 or (resid 896 and (name N or name CA or \ name C or name O or name CB )) or resid 897 through 905 or (resid 906 through 90 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 908 through \ 909 or (resid 910 and (name N or name CA or name C or name O or name CB )) or re \ sid 911 through 912 or (resid 913 and (name N or name CA or name C or name O or \ name CB )) or resid 914 through 929 or (resid 930 through 934 and (name N or nam \ e CA or name C or name O or name CB )) or resid 935 or (resid 936 through 937 an \ d (name N or name CA or name C or name O or name CB )) or resid 938 through 952 \ or (resid 953 and (name N or name CA or name C or name O or name CB )) or resid \ 954 through 972 or (resid 973 through 974 and (name N or name CA or name C or na \ me O or name CB )) or resid 975 or (resid 976 and (name N or name CA or name C o \ r name O or name CB )) or resid 977 through 981 or (resid 982 and (name N or nam \ e CA or name C or name O or name CB )) or resid 983 through 985 or (resid 986 an \ d (name N or name CA or name C or name O or name CB )) or resid 987 through 988 \ or (resid 989 and (name N or name CA or name C or name O or name CB )) or resid \ 990 through 993 or (resid 994 through 995 and (name N or name CA or name C or na \ me O or name CB )) or resid 996 through 1005)) } 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: 8.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.980 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 : 0.006 0.088 20111 Z= 0.312 Angle : 0.882 9.488 27328 Z= 0.530 Chirality : 0.053 0.258 3060 Planarity : 0.006 0.064 3463 Dihedral : 9.869 74.247 6928 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.73 % Favored : 96.15 % Rotamer: Outliers : 0.46 % Allowed : 3.17 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.39 (0.11), residues: 2522 helix: -4.35 (0.06), residues: 1406 sheet: -2.27 (0.63), residues: 52 loop : -2.25 (0.16), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 285 TYR 0.032 0.002 TYR C 912 PHE 0.041 0.003 PHE C 678 TRP 0.027 0.003 TRP C 601 HIS 0.015 0.002 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00631 (20111) covalent geometry : angle 0.88213 (27328) hydrogen bonds : bond 0.30512 ( 836) hydrogen bonds : angle 9.73650 ( 2397) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 491 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 997 LEU cc_start: 0.9254 (tp) cc_final: 0.8884 (tm) outliers start: 9 outliers final: 6 residues processed: 495 average time/residue: 0.5757 time to fit residues: 322.7207 Evaluate side-chains 225 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 219 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain C residue 255 ASN Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 992 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 0.0770 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 202 ASN A 297 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 ASN B 192 ASN C 109 GLN C 226 ASN ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 654 ASN C 939 GLN C 990 ASN D 89 GLN D 332 HIS D 386 ASN ** D 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 681 GLN ** D 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.107540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.074243 restraints weight = 48911.964| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.23 r_work: 0.3069 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20111 Z= 0.127 Angle : 0.609 11.931 27328 Z= 0.320 Chirality : 0.042 0.164 3060 Planarity : 0.005 0.061 3463 Dihedral : 5.232 68.022 2780 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.86 % Allowed : 13.53 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.10 (0.14), residues: 2522 helix: -2.19 (0.11), residues: 1432 sheet: -2.73 (0.59), residues: 42 loop : -1.59 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 802 TYR 0.016 0.001 TYR A 190 PHE 0.028 0.002 PHE B 91 TRP 0.014 0.001 TRP A 60 HIS 0.008 0.001 HIS C 852 Details of bonding type rmsd covalent geometry : bond 0.00280 (20111) covalent geometry : angle 0.60909 (27328) hydrogen bonds : bond 0.04191 ( 836) hydrogen bonds : angle 4.91094 ( 2397) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 251 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8788 (mp0) cc_final: 0.8500 (mp0) REVERT: A 32 GLU cc_start: 0.8866 (mp0) cc_final: 0.8563 (mp0) REVERT: A 61 ARG cc_start: 0.9114 (mpt-90) cc_final: 0.8794 (mpp80) REVERT: A 105 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8919 (tptm) REVERT: A 165 ARG cc_start: 0.8894 (ptm160) cc_final: 0.8551 (ptm160) REVERT: B 104 LEU cc_start: 0.8920 (mt) cc_final: 0.8086 (pp) REVERT: C 307 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8541 (pt0) REVERT: C 775 ILE cc_start: 0.9363 (mt) cc_final: 0.9143 (tp) REVERT: C 791 TYR cc_start: 0.7089 (t80) cc_final: 0.6741 (t80) REVERT: C 809 LYS cc_start: 0.9198 (mmmt) cc_final: 0.8727 (mmmt) REVERT: C 827 LEU cc_start: 0.8257 (mt) cc_final: 0.7995 (mm) REVERT: C 921 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8431 (m-80) REVERT: C 943 PHE cc_start: 0.8314 (m-80) cc_final: 0.7604 (m-80) REVERT: D 86 ARG cc_start: 0.8562 (ptt90) cc_final: 0.8170 (mtm180) REVERT: D 156 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8699 (pm20) REVERT: D 335 GLU cc_start: 0.8499 (mp0) cc_final: 0.8245 (mp0) outliers start: 56 outliers final: 14 residues processed: 291 average time/residue: 0.5624 time to fit residues: 187.4117 Evaluate side-chains 220 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 255 ASN Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 826 CYS Chi-restraints excluded: chain C residue 921 PHE Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 349 HIS Chi-restraints excluded: chain D residue 492 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 104 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 HIS B 93 ASN ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN C 782 GLN C 979 HIS D 93 ASN ** D 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 973 ASN ** D 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.102778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.068953 restraints weight = 49568.863| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.15 r_work: 0.2956 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20111 Z= 0.227 Angle : 0.629 8.742 27328 Z= 0.326 Chirality : 0.044 0.145 3060 Planarity : 0.004 0.036 3463 Dihedral : 4.920 67.832 2773 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.12 % Allowed : 14.81 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.16), residues: 2522 helix: -0.82 (0.13), residues: 1442 sheet: -2.74 (0.47), residues: 86 loop : -1.45 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 359 TYR 0.021 0.002 TYR C 755 PHE 0.028 0.002 PHE C 699 TRP 0.013 0.001 TRP C 757 HIS 0.008 0.002 HIS C 881 Details of bonding type rmsd covalent geometry : bond 0.00530 (20111) covalent geometry : angle 0.62946 (27328) hydrogen bonds : bond 0.04184 ( 836) hydrogen bonds : angle 4.48672 ( 2397) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 216 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.9211 (mpt-90) cc_final: 0.8990 (mpt-90) REVERT: A 105 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.8817 (tptt) REVERT: A 117 ILE cc_start: 0.8582 (mm) cc_final: 0.8292 (mm) REVERT: A 145 ARG cc_start: 0.9247 (tpp80) cc_final: 0.8865 (tpp80) REVERT: A 175 ARG cc_start: 0.9353 (OUTLIER) cc_final: 0.8697 (mtm110) REVERT: A 231 TRP cc_start: 0.8053 (t60) cc_final: 0.7756 (t60) REVERT: A 234 LYS cc_start: 0.7875 (mmpt) cc_final: 0.7573 (mtpt) REVERT: B 104 LEU cc_start: 0.9110 (mt) cc_final: 0.8623 (pp) REVERT: B 134 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.8092 (p90) REVERT: B 223 TYR cc_start: 0.8359 (OUTLIER) cc_final: 0.8035 (t80) REVERT: C 50 VAL cc_start: 0.9198 (OUTLIER) cc_final: 0.8986 (p) REVERT: C 147 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7304 (pmmt) REVERT: C 233 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8905 (ttm-80) REVERT: C 484 SER cc_start: 0.9228 (OUTLIER) cc_final: 0.8978 (t) REVERT: C 491 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8289 (tm-30) REVERT: C 791 TYR cc_start: 0.7689 (t80) cc_final: 0.7313 (t80) REVERT: C 866 MET cc_start: 0.8875 (ppp) cc_final: 0.8500 (pmt) REVERT: C 921 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8463 (m-80) REVERT: C 943 PHE cc_start: 0.8354 (m-80) cc_final: 0.7829 (m-80) outliers start: 61 outliers final: 20 residues processed: 254 average time/residue: 0.5780 time to fit residues: 168.3470 Evaluate side-chains 216 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 491 GLN Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 826 CYS Chi-restraints excluded: chain C residue 920 TYR Chi-restraints excluded: chain C residue 921 PHE Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1002 ASN Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 349 HIS Chi-restraints excluded: chain D residue 390 LYS Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 792 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 2 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 140 optimal weight: 30.0000 chunk 148 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 101 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 241 optimal weight: 20.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.104029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.070793 restraints weight = 49731.278| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.11 r_work: 0.2981 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20111 Z= 0.176 Angle : 0.577 8.447 27328 Z= 0.296 Chirality : 0.043 0.160 3060 Planarity : 0.003 0.037 3463 Dihedral : 4.718 67.139 2771 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.86 % Allowed : 16.09 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.16), residues: 2522 helix: -0.19 (0.14), residues: 1435 sheet: -2.41 (0.44), residues: 110 loop : -1.37 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 145 TYR 0.017 0.001 TYR D 223 PHE 0.023 0.001 PHE C 916 TRP 0.013 0.001 TRP D 143 HIS 0.005 0.001 HIS C 415 Details of bonding type rmsd covalent geometry : bond 0.00412 (20111) covalent geometry : angle 0.57672 (27328) hydrogen bonds : bond 0.03583 ( 836) hydrogen bonds : angle 4.27749 ( 2397) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 201 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8244 (tm-30) cc_final: 0.8036 (tm-30) REVERT: A 35 GLU cc_start: 0.9396 (tm-30) cc_final: 0.9137 (tm-30) REVERT: A 41 LYS cc_start: 0.8832 (ptmm) cc_final: 0.8063 (mtmm) REVERT: A 105 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8965 (tptp) REVERT: A 145 ARG cc_start: 0.9264 (tpp80) cc_final: 0.9012 (tpp80) REVERT: A 152 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9113 (pp) REVERT: A 165 ARG cc_start: 0.8806 (ptm160) cc_final: 0.8455 (ptm160) REVERT: A 166 TYR cc_start: 0.8458 (m-80) cc_final: 0.8036 (m-80) REVERT: A 175 ARG cc_start: 0.9342 (OUTLIER) cc_final: 0.8689 (mtm110) REVERT: A 231 TRP cc_start: 0.8076 (t60) cc_final: 0.7791 (t60) REVERT: A 234 LYS cc_start: 0.7785 (mmpt) cc_final: 0.7534 (mtmt) REVERT: A 236 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7709 (tm-30) REVERT: B 104 LEU cc_start: 0.9138 (mt) cc_final: 0.8698 (pp) REVERT: B 134 TYR cc_start: 0.8714 (OUTLIER) cc_final: 0.7945 (p90) REVERT: B 223 TYR cc_start: 0.8330 (OUTLIER) cc_final: 0.7988 (t80) REVERT: C 98 MET cc_start: 0.8863 (mmm) cc_final: 0.8527 (tpt) REVERT: C 147 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7241 (pmmt) REVERT: C 791 TYR cc_start: 0.7818 (t80) cc_final: 0.7504 (t80) REVERT: C 857 LYS cc_start: 0.8783 (mtmt) cc_final: 0.8485 (mtpp) REVERT: C 921 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8528 (m-80) outliers start: 56 outliers final: 28 residues processed: 238 average time/residue: 0.5649 time to fit residues: 154.6795 Evaluate side-chains 211 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 826 CYS Chi-restraints excluded: chain C residue 838 LEU Chi-restraints excluded: chain C residue 920 TYR Chi-restraints excluded: chain C residue 921 PHE Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1002 ASN Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 349 HIS Chi-restraints excluded: chain D residue 390 LYS Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 792 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 241 optimal weight: 50.0000 chunk 148 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 178 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN ** D 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.102994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.069107 restraints weight = 49270.996| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.17 r_work: 0.2963 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20111 Z= 0.163 Angle : 0.571 9.914 27328 Z= 0.289 Chirality : 0.042 0.133 3060 Planarity : 0.003 0.035 3463 Dihedral : 4.571 66.879 2771 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.91 % Allowed : 16.34 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.17), residues: 2522 helix: 0.20 (0.14), residues: 1432 sheet: -2.42 (0.43), residues: 110 loop : -1.28 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 802 TYR 0.019 0.001 TYR D 920 PHE 0.022 0.001 PHE C 699 TRP 0.016 0.001 TRP A 60 HIS 0.010 0.001 HIS D 979 Details of bonding type rmsd covalent geometry : bond 0.00381 (20111) covalent geometry : angle 0.57135 (27328) hydrogen bonds : bond 0.03356 ( 836) hydrogen bonds : angle 4.13647 ( 2397) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 208 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8220 (tm-30) REVERT: A 35 GLU cc_start: 0.9439 (tm-30) cc_final: 0.9173 (tm-30) REVERT: A 41 LYS cc_start: 0.8771 (ptmm) cc_final: 0.7995 (mtmm) REVERT: A 61 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8766 (ttm-80) REVERT: A 105 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8829 (tptp) REVERT: A 145 ARG cc_start: 0.9256 (tpp80) cc_final: 0.8833 (mmm160) REVERT: A 152 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9095 (pp) REVERT: A 165 ARG cc_start: 0.8828 (ptm160) cc_final: 0.8429 (ptm160) REVERT: A 215 PHE cc_start: 0.8501 (m-80) cc_final: 0.7959 (m-10) REVERT: A 231 TRP cc_start: 0.8082 (t60) cc_final: 0.7827 (t60) REVERT: A 236 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: B 41 LYS cc_start: 0.8866 (mmmm) cc_final: 0.8397 (tmtt) REVERT: B 104 LEU cc_start: 0.9141 (mt) cc_final: 0.8765 (pp) REVERT: B 134 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.8024 (p90) REVERT: B 145 ARG cc_start: 0.8787 (mmm160) cc_final: 0.8556 (mmp80) REVERT: B 222 ASP cc_start: 0.7072 (m-30) cc_final: 0.6866 (m-30) REVERT: B 223 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.7988 (t80) REVERT: C 98 MET cc_start: 0.8909 (mmm) cc_final: 0.8552 (tpt) REVERT: C 147 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7259 (pmmt) REVERT: C 307 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8538 (pt0) REVERT: C 484 SER cc_start: 0.9149 (OUTLIER) cc_final: 0.8891 (t) REVERT: C 564 LYS cc_start: 0.8537 (ttpp) cc_final: 0.8223 (ttpp) REVERT: C 791 TYR cc_start: 0.7889 (t80) cc_final: 0.7574 (t80) REVERT: C 809 LYS cc_start: 0.9088 (mmmt) cc_final: 0.8454 (mmmt) REVERT: C 857 LYS cc_start: 0.8923 (mtmt) cc_final: 0.8630 (mtpp) REVERT: C 866 MET cc_start: 0.8872 (ppp) cc_final: 0.8458 (pmt) REVERT: C 921 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8564 (m-80) REVERT: C 943 PHE cc_start: 0.8292 (m-80) cc_final: 0.7750 (m-80) REVERT: C 1001 MET cc_start: 0.8459 (mmm) cc_final: 0.8213 (mmm) REVERT: C 1004 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8065 (m-10) outliers start: 57 outliers final: 24 residues processed: 247 average time/residue: 0.6130 time to fit residues: 173.3836 Evaluate side-chains 220 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 826 CYS Chi-restraints excluded: chain C residue 838 LEU Chi-restraints excluded: chain C residue 920 TYR Chi-restraints excluded: chain C residue 921 PHE Chi-restraints excluded: chain C residue 1002 ASN Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 349 HIS Chi-restraints excluded: chain D residue 390 LYS Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 504 TYR Chi-restraints excluded: chain D residue 695 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 162 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 143 optimal weight: 30.0000 chunk 165 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 32 optimal weight: 0.2980 chunk 80 optimal weight: 4.9990 chunk 249 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN C 263 ASN ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 786 HIS ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 975 HIS D 979 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.103381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.069673 restraints weight = 49073.537| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.14 r_work: 0.2977 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20111 Z= 0.140 Angle : 0.560 10.414 27328 Z= 0.282 Chirality : 0.042 0.129 3060 Planarity : 0.003 0.044 3463 Dihedral : 4.441 66.692 2769 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.01 % Allowed : 16.55 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.17), residues: 2522 helix: 0.44 (0.14), residues: 1446 sheet: -2.42 (0.43), residues: 110 loop : -1.20 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 802 TYR 0.030 0.001 TYR D 888 PHE 0.018 0.001 PHE C 699 TRP 0.018 0.001 TRP D 143 HIS 0.008 0.001 HIS D 979 Details of bonding type rmsd covalent geometry : bond 0.00327 (20111) covalent geometry : angle 0.55986 (27328) hydrogen bonds : bond 0.03169 ( 836) hydrogen bonds : angle 4.06777 ( 2397) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 196 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8219 (tm-30) REVERT: A 41 LYS cc_start: 0.8770 (ptmm) cc_final: 0.8030 (mtmm) REVERT: A 105 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8817 (tptp) REVERT: A 145 ARG cc_start: 0.9223 (tpp80) cc_final: 0.8826 (mmm160) REVERT: A 152 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9125 (pp) REVERT: A 165 ARG cc_start: 0.8821 (ptm160) cc_final: 0.8428 (ptm160) REVERT: A 215 PHE cc_start: 0.8513 (m-80) cc_final: 0.7967 (m-10) REVERT: A 231 TRP cc_start: 0.8107 (t60) cc_final: 0.7865 (t60) REVERT: A 236 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: B 41 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8416 (tmtt) REVERT: B 104 LEU cc_start: 0.9137 (mt) cc_final: 0.8835 (pp) REVERT: B 105 LYS cc_start: 0.9010 (tttm) cc_final: 0.8582 (tmmt) REVERT: B 134 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.8109 (p90) REVERT: B 222 ASP cc_start: 0.7088 (m-30) cc_final: 0.6872 (m-30) REVERT: B 223 TYR cc_start: 0.8356 (OUTLIER) cc_final: 0.7970 (t80) REVERT: B 291 ASP cc_start: 0.9397 (m-30) cc_final: 0.9196 (m-30) REVERT: C 98 MET cc_start: 0.8890 (mmm) cc_final: 0.8491 (tpt) REVERT: C 145 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8375 (mmt90) REVERT: C 147 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7222 (pmmt) REVERT: C 307 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8474 (pt0) REVERT: C 484 SER cc_start: 0.9165 (OUTLIER) cc_final: 0.8907 (t) REVERT: C 564 LYS cc_start: 0.8512 (ttpp) cc_final: 0.8293 (ttpp) REVERT: C 791 TYR cc_start: 0.7990 (t80) cc_final: 0.7725 (t80) REVERT: C 809 LYS cc_start: 0.9089 (mmmt) cc_final: 0.8450 (mmmt) REVERT: C 857 LYS cc_start: 0.8935 (mtmt) cc_final: 0.8618 (mtpp) REVERT: C 866 MET cc_start: 0.8920 (ppp) cc_final: 0.8517 (pmt) REVERT: C 921 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8671 (m-80) REVERT: C 943 PHE cc_start: 0.8290 (m-80) cc_final: 0.7818 (m-80) REVERT: C 961 ASN cc_start: 0.9523 (m110) cc_final: 0.9282 (m110) REVERT: C 1004 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.7996 (m-10) outliers start: 59 outliers final: 35 residues processed: 240 average time/residue: 0.5788 time to fit residues: 159.1791 Evaluate side-chains 223 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 177 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 647 MET Chi-restraints excluded: chain C residue 826 CYS Chi-restraints excluded: chain C residue 838 LEU Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 920 TYR Chi-restraints excluded: chain C residue 921 PHE Chi-restraints excluded: chain C residue 1002 ASN Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 349 HIS Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 504 TYR Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 792 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 46 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 203 optimal weight: 6.9990 chunk 216 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 247 optimal weight: 1.9990 chunk 187 optimal weight: 0.4980 chunk 230 optimal weight: 0.6980 chunk 227 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN C 263 ASN ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 975 HIS ** D 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.103922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.070275 restraints weight = 49485.205| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.16 r_work: 0.2993 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20111 Z= 0.117 Angle : 0.557 11.281 27328 Z= 0.278 Chirality : 0.041 0.130 3060 Planarity : 0.003 0.049 3463 Dihedral : 4.328 66.650 2769 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.71 % Allowed : 17.26 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.17), residues: 2522 helix: 0.68 (0.14), residues: 1435 sheet: -2.22 (0.44), residues: 106 loop : -1.04 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 802 TYR 0.030 0.001 TYR D 888 PHE 0.025 0.001 PHE D 522 TRP 0.020 0.001 TRP D 143 HIS 0.012 0.001 HIS D 979 Details of bonding type rmsd covalent geometry : bond 0.00274 (20111) covalent geometry : angle 0.55674 (27328) hydrogen bonds : bond 0.02987 ( 836) hydrogen bonds : angle 3.98729 ( 2397) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 196 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8898 (mp0) REVERT: A 32 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8271 (tm-30) REVERT: A 41 LYS cc_start: 0.8784 (ptmm) cc_final: 0.8072 (mtmm) REVERT: A 105 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8797 (tptp) REVERT: A 152 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9125 (pp) REVERT: A 165 ARG cc_start: 0.8830 (ptm160) cc_final: 0.8451 (ptm160) REVERT: A 173 ASP cc_start: 0.8285 (t70) cc_final: 0.7863 (p0) REVERT: A 175 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.8566 (mtm110) REVERT: A 215 PHE cc_start: 0.8488 (m-80) cc_final: 0.7958 (m-10) REVERT: A 236 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: A 254 GLU cc_start: 0.6846 (tp30) cc_final: 0.6508 (tp30) REVERT: B 41 LYS cc_start: 0.8861 (mmmm) cc_final: 0.8408 (tmtt) REVERT: B 69 GLU cc_start: 0.8459 (tp30) cc_final: 0.8247 (tp30) REVERT: B 104 LEU cc_start: 0.9129 (mt) cc_final: 0.8866 (pp) REVERT: B 105 LYS cc_start: 0.9052 (tttm) cc_final: 0.8633 (tmmt) REVERT: B 134 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.8134 (p90) REVERT: B 145 ARG cc_start: 0.8718 (mmp80) cc_final: 0.8299 (tmm160) REVERT: B 175 ARG cc_start: 0.9428 (mtp85) cc_final: 0.9111 (mtm180) REVERT: B 222 ASP cc_start: 0.7073 (m-30) cc_final: 0.6859 (m-30) REVERT: B 223 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.7960 (t80) REVERT: B 291 ASP cc_start: 0.9399 (m-30) cc_final: 0.9186 (m-30) REVERT: C 98 MET cc_start: 0.8915 (mmm) cc_final: 0.8509 (tpt) REVERT: C 307 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8516 (pt0) REVERT: C 491 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8400 (tm-30) REVERT: C 647 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8207 (ttm) REVERT: C 791 TYR cc_start: 0.7978 (t80) cc_final: 0.7726 (t80) REVERT: C 809 LYS cc_start: 0.9058 (mmmt) cc_final: 0.8501 (mmmt) REVERT: C 857 LYS cc_start: 0.8980 (mtmt) cc_final: 0.8677 (mtpp) REVERT: C 866 MET cc_start: 0.8924 (ppp) cc_final: 0.8552 (pmt) REVERT: C 921 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8737 (m-80) REVERT: C 943 PHE cc_start: 0.8258 (m-80) cc_final: 0.7888 (m-80) REVERT: C 965 LYS cc_start: 0.9665 (tppt) cc_final: 0.9379 (tppt) REVERT: C 1004 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.7956 (m-10) REVERT: D 631 ILE cc_start: 0.2618 (OUTLIER) cc_final: 0.2030 (mp) REVERT: D 839 PHE cc_start: 0.8339 (t80) cc_final: 0.8133 (t80) outliers start: 53 outliers final: 29 residues processed: 234 average time/residue: 0.6174 time to fit residues: 165.1143 Evaluate side-chains 215 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 491 GLN Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 647 MET Chi-restraints excluded: chain C residue 826 CYS Chi-restraints excluded: chain C residue 838 LEU Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 920 TYR Chi-restraints excluded: chain C residue 921 PHE Chi-restraints excluded: chain C residue 1002 ASN Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 349 HIS Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 504 TYR Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 792 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 226 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 chunk 68 optimal weight: 0.3980 chunk 135 optimal weight: 0.1980 chunk 110 optimal weight: 6.9990 chunk 108 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 199 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 GLN ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 HIS D 975 HIS ** D 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.105032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.071675 restraints weight = 48936.661| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.16 r_work: 0.3017 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20111 Z= 0.101 Angle : 0.560 11.281 27328 Z= 0.278 Chirality : 0.041 0.153 3060 Planarity : 0.003 0.054 3463 Dihedral : 4.236 66.595 2769 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.30 % Allowed : 17.72 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.17), residues: 2522 helix: 0.84 (0.15), residues: 1437 sheet: -2.10 (0.46), residues: 96 loop : -0.99 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 802 TYR 0.030 0.001 TYR D 888 PHE 0.019 0.001 PHE D 522 TRP 0.040 0.002 TRP A 231 HIS 0.013 0.001 HIS D 979 Details of bonding type rmsd covalent geometry : bond 0.00230 (20111) covalent geometry : angle 0.56018 (27328) hydrogen bonds : bond 0.02839 ( 836) hydrogen bonds : angle 3.91717 ( 2397) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 0.856 Fit side-chains REVERT: A 41 LYS cc_start: 0.8753 (ptmm) cc_final: 0.8066 (mtmm) REVERT: A 86 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7344 (tmm160) REVERT: A 105 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8723 (tptt) REVERT: A 152 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9141 (pp) REVERT: A 165 ARG cc_start: 0.8826 (ptm160) cc_final: 0.8440 (ptm160) REVERT: A 173 ASP cc_start: 0.8237 (t70) cc_final: 0.7896 (p0) REVERT: A 175 ARG cc_start: 0.9348 (OUTLIER) cc_final: 0.8566 (mtm110) REVERT: A 215 PHE cc_start: 0.8494 (m-80) cc_final: 0.8002 (m-10) REVERT: A 236 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7769 (tm-30) REVERT: B 41 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8448 (tmtt) REVERT: B 68 GLU cc_start: 0.8978 (tp30) cc_final: 0.8723 (tp30) REVERT: B 74 PRO cc_start: 0.8629 (Cg_endo) cc_final: 0.8162 (Cg_exo) REVERT: B 104 LEU cc_start: 0.9124 (mt) cc_final: 0.8858 (pp) REVERT: B 105 LYS cc_start: 0.9079 (tttm) cc_final: 0.8681 (tmmt) REVERT: B 134 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.8249 (p90) REVERT: B 145 ARG cc_start: 0.8685 (mmp80) cc_final: 0.8255 (tmm160) REVERT: B 223 TYR cc_start: 0.8315 (OUTLIER) cc_final: 0.7919 (t80) REVERT: B 291 ASP cc_start: 0.9406 (m-30) cc_final: 0.9188 (m-30) REVERT: C 98 MET cc_start: 0.8911 (mmm) cc_final: 0.8540 (tpt) REVERT: C 262 GLU cc_start: 0.8676 (tp30) cc_final: 0.8380 (mm-30) REVERT: C 307 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8416 (pt0) REVERT: C 647 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8191 (ttm) REVERT: C 791 TYR cc_start: 0.7966 (t80) cc_final: 0.7706 (t80) REVERT: C 809 LYS cc_start: 0.9009 (mmmt) cc_final: 0.8424 (mmmt) REVERT: C 811 PHE cc_start: 0.8929 (m-80) cc_final: 0.8661 (m-10) REVERT: C 839 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8848 (m-80) REVERT: C 857 LYS cc_start: 0.9021 (mtmt) cc_final: 0.8712 (mtpp) REVERT: C 866 MET cc_start: 0.8956 (ppp) cc_final: 0.8571 (pmt) REVERT: C 921 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8766 (m-80) REVERT: C 943 PHE cc_start: 0.8243 (m-80) cc_final: 0.7880 (m-80) REVERT: C 1004 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.7944 (m-10) REVERT: D 839 PHE cc_start: 0.8343 (t80) cc_final: 0.8127 (t80) outliers start: 45 outliers final: 27 residues processed: 221 average time/residue: 0.5886 time to fit residues: 150.1349 Evaluate side-chains 214 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 647 MET Chi-restraints excluded: chain C residue 810 HIS Chi-restraints excluded: chain C residue 826 CYS Chi-restraints excluded: chain C residue 838 LEU Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 920 TYR Chi-restraints excluded: chain C residue 921 PHE Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 349 HIS Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 504 TYR Chi-restraints excluded: chain D residue 695 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 49 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 4 optimal weight: 0.4980 chunk 227 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 HIS D 975 HIS ** D 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.101111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.067384 restraints weight = 49335.130| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.14 r_work: 0.2928 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 20111 Z= 0.275 Angle : 0.670 10.780 27328 Z= 0.340 Chirality : 0.045 0.143 3060 Planarity : 0.003 0.056 3463 Dihedral : 4.566 66.069 2769 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.01 % Allowed : 17.26 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.17), residues: 2522 helix: 0.55 (0.14), residues: 1444 sheet: -2.45 (0.44), residues: 100 loop : -1.09 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 802 TYR 0.029 0.002 TYR D 888 PHE 0.026 0.002 PHE C 699 TRP 0.065 0.003 TRP A 231 HIS 0.012 0.002 HIS D 979 Details of bonding type rmsd covalent geometry : bond 0.00639 (20111) covalent geometry : angle 0.67013 (27328) hydrogen bonds : bond 0.03838 ( 836) hydrogen bonds : angle 4.30359 ( 2397) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 175 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8839 (tptp) REVERT: A 134 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.8446 (p90) REVERT: A 152 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9161 (pp) REVERT: A 175 ARG cc_start: 0.9416 (OUTLIER) cc_final: 0.8796 (mtm110) REVERT: A 215 PHE cc_start: 0.8491 (m-80) cc_final: 0.8021 (m-10) REVERT: A 236 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7831 (tm-30) REVERT: B 68 GLU cc_start: 0.8870 (tp30) cc_final: 0.8662 (tp30) REVERT: B 74 PRO cc_start: 0.8608 (Cg_endo) cc_final: 0.8225 (Cg_exo) REVERT: B 104 LEU cc_start: 0.9130 (mt) cc_final: 0.8904 (mt) REVERT: B 105 LYS cc_start: 0.9171 (tttm) cc_final: 0.8854 (tmmt) REVERT: B 134 TYR cc_start: 0.8843 (OUTLIER) cc_final: 0.8123 (p90) REVERT: B 175 ARG cc_start: 0.9453 (mtm180) cc_final: 0.9201 (mtm180) REVERT: B 291 ASP cc_start: 0.9400 (m-30) cc_final: 0.9118 (m-30) REVERT: C 98 MET cc_start: 0.9010 (mmm) cc_final: 0.8681 (tpt) REVERT: C 195 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8577 (tt0) REVERT: C 491 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8362 (tm-30) REVERT: C 791 TYR cc_start: 0.7904 (t80) cc_final: 0.7586 (t80) REVERT: C 857 LYS cc_start: 0.9048 (mtmt) cc_final: 0.8782 (mtpp) REVERT: C 866 MET cc_start: 0.8956 (ppp) cc_final: 0.8597 (pmt) REVERT: C 921 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8732 (m-80) REVERT: C 943 PHE cc_start: 0.8271 (m-80) cc_final: 0.7901 (m-80) REVERT: C 961 ASN cc_start: 0.9518 (m110) cc_final: 0.9266 (m110) REVERT: C 965 LYS cc_start: 0.9685 (tppt) cc_final: 0.9370 (tptp) REVERT: D 857 LYS cc_start: 0.9194 (mmpt) cc_final: 0.8978 (mppt) REVERT: D 919 TRP cc_start: 0.9066 (m-10) cc_final: 0.8482 (m-90) REVERT: D 1004 PHE cc_start: 0.8374 (m-80) cc_final: 0.7637 (m-80) outliers start: 59 outliers final: 31 residues processed: 217 average time/residue: 0.5648 time to fit residues: 141.4674 Evaluate side-chains 212 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 491 GLN Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 647 MET Chi-restraints excluded: chain C residue 810 HIS Chi-restraints excluded: chain C residue 826 CYS Chi-restraints excluded: chain C residue 838 LEU Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain C residue 920 TYR Chi-restraints excluded: chain C residue 921 PHE Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 349 HIS Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 792 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 80 optimal weight: 0.7980 chunk 237 optimal weight: 7.9990 chunk 70 optimal weight: 0.0370 chunk 50 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 242 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 chunk 212 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 HIS D 975 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.104092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.070693 restraints weight = 49155.870| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.16 r_work: 0.3003 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20111 Z= 0.110 Angle : 0.593 12.149 27328 Z= 0.295 Chirality : 0.041 0.144 3060 Planarity : 0.003 0.060 3463 Dihedral : 4.378 66.356 2769 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.84 % Allowed : 18.64 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.17), residues: 2522 helix: 0.89 (0.15), residues: 1419 sheet: -2.20 (0.45), residues: 96 loop : -0.92 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 802 TYR 0.030 0.001 TYR D 888 PHE 0.035 0.001 PHE D 949 TRP 0.077 0.002 TRP A 231 HIS 0.013 0.001 HIS D 979 Details of bonding type rmsd covalent geometry : bond 0.00254 (20111) covalent geometry : angle 0.59266 (27328) hydrogen bonds : bond 0.02981 ( 836) hydrogen bonds : angle 4.00863 ( 2397) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8307 (tm-30) REVERT: A 105 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8984 (tptm) REVERT: A 134 TYR cc_start: 0.8678 (OUTLIER) cc_final: 0.8464 (p90) REVERT: A 152 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9146 (pp) REVERT: A 165 ARG cc_start: 0.8852 (ptm160) cc_final: 0.8561 (ptm160) REVERT: A 175 ARG cc_start: 0.9373 (OUTLIER) cc_final: 0.8746 (mtm110) REVERT: A 215 PHE cc_start: 0.8501 (m-80) cc_final: 0.7976 (m-10) REVERT: A 236 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7770 (tm-30) REVERT: B 41 LYS cc_start: 0.8852 (mmmm) cc_final: 0.8398 (tmtt) REVERT: B 68 GLU cc_start: 0.8934 (tp30) cc_final: 0.8689 (tp30) REVERT: B 74 PRO cc_start: 0.8581 (Cg_endo) cc_final: 0.8133 (Cg_exo) REVERT: B 104 LEU cc_start: 0.9098 (mt) cc_final: 0.8893 (pp) REVERT: B 105 LYS cc_start: 0.9163 (tttm) cc_final: 0.8821 (tmmt) REVERT: B 134 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.8142 (p90) REVERT: C 98 MET cc_start: 0.8922 (mmm) cc_final: 0.8585 (tpt) REVERT: C 262 GLU cc_start: 0.8761 (tp30) cc_final: 0.8390 (mm-30) REVERT: C 491 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8391 (tm-30) REVERT: C 791 TYR cc_start: 0.7922 (t80) cc_final: 0.7642 (t80) REVERT: C 809 LYS cc_start: 0.9099 (mmmt) cc_final: 0.8415 (mmmt) REVERT: C 811 PHE cc_start: 0.8894 (m-80) cc_final: 0.8653 (m-10) REVERT: C 839 PHE cc_start: 0.9233 (t80) cc_final: 0.8743 (m-80) REVERT: C 857 LYS cc_start: 0.9068 (mtmt) cc_final: 0.8672 (mtpp) REVERT: C 866 MET cc_start: 0.8964 (ppp) cc_final: 0.8593 (pmt) REVERT: C 921 PHE cc_start: 0.9097 (OUTLIER) cc_final: 0.8750 (m-80) REVERT: C 943 PHE cc_start: 0.8183 (m-80) cc_final: 0.7846 (m-80) REVERT: C 965 LYS cc_start: 0.9659 (tppt) cc_final: 0.9382 (tptp) REVERT: D 645 PHE cc_start: 0.7344 (t80) cc_final: 0.7009 (m-80) REVERT: D 912 TYR cc_start: 0.8253 (m-80) cc_final: 0.7603 (m-10) REVERT: D 919 TRP cc_start: 0.9080 (m-10) cc_final: 0.8496 (m-90) REVERT: D 930 MET cc_start: 0.7240 (pmm) cc_final: 0.6757 (mtm) REVERT: D 1004 PHE cc_start: 0.8290 (m-80) cc_final: 0.8087 (m-80) outliers start: 36 outliers final: 20 residues processed: 210 average time/residue: 0.5083 time to fit residues: 123.5363 Evaluate side-chains 198 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 491 GLN Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 826 CYS Chi-restraints excluded: chain C residue 838 LEU Chi-restraints excluded: chain C residue 920 TYR Chi-restraints excluded: chain C residue 921 PHE Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 349 HIS Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 792 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 14 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 111 optimal weight: 0.9980 chunk 212 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 104 optimal weight: 0.3980 chunk 181 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 213 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 HIS D 975 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.103229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.069720 restraints weight = 49304.462| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.15 r_work: 0.2979 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20111 Z= 0.147 Angle : 0.606 11.692 27328 Z= 0.303 Chirality : 0.042 0.162 3060 Planarity : 0.003 0.059 3463 Dihedral : 4.356 66.444 2769 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.99 % Allowed : 19.00 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.17), residues: 2522 helix: 0.91 (0.15), residues: 1423 sheet: -2.24 (0.45), residues: 96 loop : -0.89 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 802 TYR 0.021 0.001 TYR D 223 PHE 0.032 0.001 PHE D 949 TRP 0.080 0.002 TRP A 231 HIS 0.006 0.001 HIS C 810 Details of bonding type rmsd covalent geometry : bond 0.00349 (20111) covalent geometry : angle 0.60626 (27328) hydrogen bonds : bond 0.03163 ( 836) hydrogen bonds : angle 4.02350 ( 2397) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7197.54 seconds wall clock time: 123 minutes 18.35 seconds (7398.35 seconds total)