Starting phenix.real_space_refine on Wed May 21 19:45:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s9t_40248/05_2025/8s9t_40248.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s9t_40248/05_2025/8s9t_40248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s9t_40248/05_2025/8s9t_40248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s9t_40248/05_2025/8s9t_40248.map" model { file = "/net/cci-nas-00/data/ceres_data/8s9t_40248/05_2025/8s9t_40248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s9t_40248/05_2025/8s9t_40248.cif" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.026 sd= 0.094 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: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 52 5.16 5 C 13731 2.51 5 N 3878 2.21 5 O 4274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21971 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 769, 6000 Classifications: {'peptide': 769} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 733} Chain breaks: 1 Chain: "B" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1487 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 177} Chain: "C" Number of atoms: 4369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4369 Classifications: {'peptide': 555} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 538} Chain: "D" Number of atoms: 3877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3877 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 25, 'TRANS': 480} Chain breaks: 2 Chain: "E" Number of atoms: 5448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5448 Classifications: {'peptide': 677} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 633} Chain breaks: 1 Chain: "F" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 790 Classifications: {'RNA': 37} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 9, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 18, 'rna3p': 18} Time building chain proxies: 14.11, per 1000 atoms: 0.64 Number of scatterers: 21971 At special positions: 0 Unit cell: (103.68, 114.21, 183.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 36 15.00 O 4274 8.00 N 3878 7.00 C 13731 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.72 Conformation dependent library (CDL) restraints added in 2.8 seconds 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4950 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 40 sheets defined 36.5% alpha, 21.2% beta 0 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 8.52 Creating SS restraints... Processing helix chain 'A' and resid 40 through 60 Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 167 through 185 Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 207 through 218 removed outlier: 3.507A pdb=" N LEU A 214 " --> pdb=" O GLN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 276 through 279 Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 421 through 431 Processing helix chain 'A' and resid 433 through 439 Processing helix chain 'A' and resid 495 through 508 removed outlier: 3.752A pdb=" N LEU A 499 " --> pdb=" O THR A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 573 Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 589 through 594 removed outlier: 3.529A pdb=" N SER A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 649 Processing helix chain 'A' and resid 650 through 659 Processing helix chain 'A' and resid 670 through 682 Processing helix chain 'A' and resid 686 through 688 No H-bonds generated for 'chain 'A' and resid 686 through 688' Processing helix chain 'A' and resid 689 through 702 removed outlier: 3.904A pdb=" N VAL A 693 " --> pdb=" O ASN A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 711 removed outlier: 4.077A pdb=" N LYS A 709 " --> pdb=" O ASN A 705 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP A 710 " --> pdb=" O ARG A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 726 Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 738 through 742 removed outlier: 3.589A pdb=" N THR A 742 " --> pdb=" O SER A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 780 removed outlier: 5.101A pdb=" N ALA A 757 " --> pdb=" O SER A 753 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLU A 758 " --> pdb=" O GLU A 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 29 Processing helix chain 'B' and resid 58 through 64 Processing helix chain 'C' and resid 10 through 16 Processing helix chain 'C' and resid 20 through 35 removed outlier: 3.830A pdb=" N THR C 35 " --> pdb=" O THR C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 48 Processing helix chain 'C' and resid 50 through 59 Processing helix chain 'C' and resid 60 through 65 removed outlier: 3.970A pdb=" N PHE C 63 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 79 removed outlier: 3.652A pdb=" N ASN C 79 " --> pdb=" O PRO C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 Processing helix chain 'C' and resid 135 through 153 Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.665A pdb=" N GLY C 160 " --> pdb=" O GLY C 157 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG C 161 " --> pdb=" O ALA C 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 157 through 161' Processing helix chain 'C' and resid 193 through 212 removed outlier: 4.038A pdb=" N LYS C 204 " --> pdb=" O ARG C 200 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA C 206 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS C 208 " --> pdb=" O LYS C 204 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER C 212 " --> pdb=" O LYS C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 229 Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 259 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 318 through 336 removed outlier: 3.521A pdb=" N THR C 336 " --> pdb=" O GLY C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.851A pdb=" N VAL C 342 " --> pdb=" O ASP C 338 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE C 343 " --> pdb=" O ASP C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 383 Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 417 through 425 Processing helix chain 'C' and resid 442 through 447 removed outlier: 3.522A pdb=" N SER C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 458 Processing helix chain 'C' and resid 459 through 472 removed outlier: 3.778A pdb=" N LEU C 463 " --> pdb=" O SER C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 494 removed outlier: 3.856A pdb=" N TYR C 494 " --> pdb=" O ARG C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 511 removed outlier: 3.559A pdb=" N ARG C 510 " --> pdb=" O LEU C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 518 Processing helix chain 'C' and resid 537 through 545 Processing helix chain 'D' and resid 47 through 63 Processing helix chain 'D' and resid 66 through 75 removed outlier: 3.630A pdb=" N LEU D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 161 Processing helix chain 'D' and resid 190 through 200 Processing helix chain 'D' and resid 206 through 213 removed outlier: 3.974A pdb=" N LEU D 210 " --> pdb=" O ASP D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 284 Processing helix chain 'D' and resid 291 through 297 removed outlier: 3.596A pdb=" N ARG D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 339 through 349 Processing helix chain 'D' and resid 355 through 364 Processing helix chain 'D' and resid 369 through 375 Processing helix chain 'D' and resid 416 through 425 Processing helix chain 'D' and resid 430 through 447 removed outlier: 4.101A pdb=" N ALA D 434 " --> pdb=" O LYS D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 483 Processing helix chain 'D' and resid 495 through 512 Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'E' and resid 193 through 209 Processing helix chain 'E' and resid 228 through 233 removed outlier: 3.723A pdb=" N GLY E 232 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 264 removed outlier: 3.834A pdb=" N ASN E 263 " --> pdb=" O PRO E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 393 Processing helix chain 'E' and resid 394 through 400 Processing helix chain 'E' and resid 414 through 419 Processing helix chain 'E' and resid 420 through 426 removed outlier: 4.092A pdb=" N LEU E 426 " --> pdb=" O GLU E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 442 Processing helix chain 'E' and resid 461 through 466 removed outlier: 3.616A pdb=" N LEU E 466 " --> pdb=" O VAL E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 removed outlier: 3.750A pdb=" N LEU E 479 " --> pdb=" O LYS E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 487 Processing helix chain 'E' and resid 536 through 540 Processing helix chain 'E' and resid 555 through 559 Processing helix chain 'E' and resid 641 through 653 Processing helix chain 'E' and resid 665 through 669 Processing helix chain 'E' and resid 679 through 682 Processing helix chain 'E' and resid 687 through 695 Processing helix chain 'E' and resid 704 through 707 Processing helix chain 'E' and resid 708 through 724 Processing helix chain 'E' and resid 732 through 744 Processing helix chain 'E' and resid 766 through 776 removed outlier: 4.006A pdb=" N PHE E 770 " --> pdb=" O ALA E 766 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.632A pdb=" N ILE A 4 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 160 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ARG A 2 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 127 Processing sheet with id=AA4, first strand: chain 'A' and resid 304 through 305 removed outlier: 6.816A pdb=" N THR A 412 " --> pdb=" O LYS A 311 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AA6, first strand: chain 'A' and resid 261 through 265 removed outlier: 6.675A pdb=" N GLU A 270 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N THR A 264 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL A 269 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N ILE A 407 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 9.878A pdb=" N CYS A 271 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA8, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA9, first strand: chain 'A' and resid 510 through 513 removed outlier: 6.598A pdb=" N LYS A 510 " --> pdb=" O GLU A 557 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 510 through 513 removed outlier: 6.598A pdb=" N LYS A 510 " --> pdb=" O GLU A 557 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 483 through 484 Processing sheet with id=AB3, first strand: chain 'A' and resid 532 through 533 Processing sheet with id=AB4, first strand: chain 'A' and resid 661 through 663 Processing sheet with id=AB5, first strand: chain 'B' and resid 45 through 49 removed outlier: 6.551A pdb=" N ASN B 91 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA B 94 " --> pdb=" O TYR B 17 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N TYR B 17 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LEU B 96 " --> pdb=" O HIS B 15 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N HIS B 15 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER B 98 " --> pdb=" O HIS B 13 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N HIS B 13 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 116 through 123 removed outlier: 6.475A pdb=" N PHE B 164 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LYS B 189 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N THR B 166 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU B 187 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU B 168 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU B 185 " --> pdb=" O GLU B 168 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TYR B 170 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 127 through 128 Processing sheet with id=AB8, first strand: chain 'C' and resid 82 through 88 removed outlier: 6.310A pdb=" N ILE C 93 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ALA C 87 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU C 121 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 180 through 183 Processing sheet with id=AC1, first strand: chain 'C' and resid 300 through 306 removed outlier: 6.431A pdb=" N THR C 311 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU C 305 " --> pdb=" O ASP C 309 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ASP C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER C 354 " --> pdb=" O ASN C 242 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 404 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 390 through 391 Processing sheet with id=AC3, first strand: chain 'C' and resid 431 through 432 Processing sheet with id=AC4, first strand: chain 'D' and resid 87 through 89 removed outlier: 3.521A pdb=" N GLY D 13 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N THR D 14 " --> pdb=" O ASP D 180 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ASP D 180 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE D 16 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU D 178 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU D 183 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 45 through 46 Processing sheet with id=AC6, first strand: chain 'D' and resid 103 through 110 removed outlier: 6.085A pdb=" N PHE D 121 " --> pdb=" O GLY D 109 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 171 through 172 removed outlier: 5.390A pdb=" N GLN D 412 " --> pdb=" O ASN D 330 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASN D 229 " --> pdb=" O VAL D 465 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N VAL D 465 " --> pdb=" O ASN D 229 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 251 through 254 Processing sheet with id=AC9, first strand: chain 'D' and resid 306 through 307 Processing sheet with id=AD1, first strand: chain 'D' and resid 378 through 385 removed outlier: 10.852A pdb=" N GLN D 378 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N SER D 399 " --> pdb=" O GLN D 378 " (cutoff:3.500A) removed outlier: 11.284A pdb=" N ALA D 380 " --> pdb=" O LEU D 397 " (cutoff:3.500A) removed outlier: 10.045A pdb=" N LEU D 397 " --> pdb=" O ALA D 380 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N HIS D 382 " --> pdb=" O GLY D 395 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N GLY D 395 " --> pdb=" O HIS D 382 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ALA D 384 " --> pdb=" O ALA D 393 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 114 through 115 Processing sheet with id=AD3, first strand: chain 'E' and resid 119 through 121 Processing sheet with id=AD4, first strand: chain 'E' and resid 501 through 508 removed outlier: 5.824A pdb=" N LEU E 501 " --> pdb=" O THR E 638 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N THR E 638 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ILE E 503 " --> pdb=" O ASP E 636 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASP E 636 " --> pdb=" O ILE E 503 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N SER E 505 " --> pdb=" O GLU E 634 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU E 634 " --> pdb=" O SER E 505 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N TYR E 149 " --> pdb=" O ASN E 639 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 501 through 508 removed outlier: 5.824A pdb=" N LEU E 501 " --> pdb=" O THR E 638 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N THR E 638 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ILE E 503 " --> pdb=" O ASP E 636 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASP E 636 " --> pdb=" O ILE E 503 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N SER E 505 " --> pdb=" O GLU E 634 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU E 634 " --> pdb=" O SER E 505 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N TYR E 149 " --> pdb=" O ASN E 639 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 172 through 174 Processing sheet with id=AD7, first strand: chain 'E' and resid 224 through 226 Processing sheet with id=AD8, first strand: chain 'E' and resid 371 through 374 removed outlier: 3.635A pdb=" N ASN E 447 " --> pdb=" O HIS E 435 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LYS E 437 " --> pdb=" O ILE E 445 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE E 445 " --> pdb=" O LYS E 437 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 269 through 272 removed outlier: 7.084A pdb=" N TRP E 270 " --> pdb=" O VAL E 312 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N GLN E 314 " --> pdb=" O TRP E 270 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ALA E 316 " --> pdb=" O PRO E 272 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP E 298 " --> pdb=" O ARG E 313 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE E 315 " --> pdb=" O ARG E 296 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG E 296 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ARG E 317 " --> pdb=" O HIS E 294 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N HIS E 294 " --> pdb=" O ARG E 317 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL E 340 " --> pdb=" O ARG E 301 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N THR E 303 " --> pdb=" O THR E 338 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N THR E 338 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 488 through 489 Processing sheet with id=AE2, first strand: chain 'E' and resid 514 through 516 Processing sheet with id=AE3, first strand: chain 'E' and resid 541 through 542 Processing sheet with id=AE4, first strand: chain 'E' and resid 607 through 608 939 hydrogen bonds defined for protein. 2538 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 8.83 Time building geometry restraints manager: 6.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4162 1.32 - 1.44: 5621 1.44 - 1.56: 12570 1.56 - 1.69: 72 1.69 - 1.81: 76 Bond restraints: 22501 Sorted by residual: bond pdb=" CB ARG A 192 " pdb=" CG ARG A 192 " ideal model delta sigma weight residual 1.520 1.424 0.096 3.00e-02 1.11e+03 1.02e+01 bond pdb=" CG ARG E 212 " pdb=" CD ARG E 212 " ideal model delta sigma weight residual 1.520 1.443 0.077 3.00e-02 1.11e+03 6.65e+00 bond pdb=" CB GLU E 206 " pdb=" CG GLU E 206 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.26e+00 bond pdb=" CB ARG B 145 " pdb=" CG ARG B 145 " ideal model delta sigma weight residual 1.520 1.446 0.074 3.00e-02 1.11e+03 6.11e+00 bond pdb=" CB ARG A 187 " pdb=" CG ARG A 187 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.89e+00 ... (remaining 22496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 29742 2.44 - 4.87: 821 4.87 - 7.31: 71 7.31 - 9.75: 11 9.75 - 12.18: 3 Bond angle restraints: 30648 Sorted by residual: angle pdb=" N SER A 531 " pdb=" CA SER A 531 " pdb=" C SER A 531 " ideal model delta sigma weight residual 110.80 122.98 -12.18 2.13e+00 2.20e-01 3.27e+01 angle pdb=" C ALA C 169 " pdb=" N GLY C 170 " pdb=" CA GLY C 170 " ideal model delta sigma weight residual 122.15 115.49 6.66 1.17e+00 7.31e-01 3.24e+01 angle pdb=" C ASN C 550 " pdb=" CA ASN C 550 " pdb=" CB ASN C 550 " ideal model delta sigma weight residual 117.23 110.26 6.97 1.36e+00 5.41e-01 2.62e+01 angle pdb=" N LEU C 165 " pdb=" CA LEU C 165 " pdb=" C LEU C 165 " ideal model delta sigma weight residual 109.64 101.67 7.97 1.56e+00 4.11e-01 2.61e+01 angle pdb=" N CYS B 45 " pdb=" CA CYS B 45 " pdb=" C CYS B 45 " ideal model delta sigma weight residual 108.02 99.14 8.88 1.75e+00 3.27e-01 2.57e+01 ... (remaining 30643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 13242 35.32 - 70.63: 296 70.63 - 105.95: 50 105.95 - 141.26: 0 141.26 - 176.58: 4 Dihedral angle restraints: 13592 sinusoidal: 5870 harmonic: 7722 Sorted by residual: dihedral pdb=" O4' U F 32 " pdb=" C1' U F 32 " pdb=" N1 U F 32 " pdb=" C2 U F 32 " ideal model delta sinusoidal sigma weight residual 200.00 23.91 176.09 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' C F 2 " pdb=" C1' C F 2 " pdb=" N1 C F 2 " pdb=" C2 C F 2 " ideal model delta sinusoidal sigma weight residual -128.00 48.58 -176.58 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U F 14 " pdb=" C1' U F 14 " pdb=" N1 U F 14 " pdb=" C2 U F 14 " ideal model delta sinusoidal sigma weight residual 232.00 61.55 170.45 1 1.70e+01 3.46e-03 6.60e+01 ... (remaining 13589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2756 0.079 - 0.158: 570 0.158 - 0.237: 54 0.237 - 0.316: 6 0.316 - 0.395: 1 Chirality restraints: 3387 Sorted by residual: chirality pdb=" CG LEU C 410 " pdb=" CB LEU C 410 " pdb=" CD1 LEU C 410 " pdb=" CD2 LEU C 410 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CG LEU B 124 " pdb=" CB LEU B 124 " pdb=" CD1 LEU B 124 " pdb=" CD2 LEU B 124 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB ILE D 298 " pdb=" CA ILE D 298 " pdb=" CG1 ILE D 298 " pdb=" CG2 ILE D 298 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 3384 not shown) Planarity restraints: 3878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 171 " 0.159 9.50e-02 1.11e+02 8.36e-02 2.69e+01 pdb=" NE ARG D 171 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG D 171 " 0.083 2.00e-02 2.50e+03 pdb=" NH1 ARG D 171 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG D 171 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 212 " -0.129 9.50e-02 1.11e+02 7.03e-02 2.21e+01 pdb=" NE ARG E 212 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG E 212 " -0.076 2.00e-02 2.50e+03 pdb=" NH1 ARG E 212 " 0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG E 212 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 221 " 0.024 2.00e-02 2.50e+03 4.65e-02 2.16e+01 pdb=" C VAL A 221 " -0.080 2.00e-02 2.50e+03 pdb=" O VAL A 221 " 0.030 2.00e-02 2.50e+03 pdb=" N ASP A 222 " 0.027 2.00e-02 2.50e+03 ... (remaining 3875 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 578 2.69 - 3.24: 21864 3.24 - 3.79: 37366 3.79 - 4.35: 52897 4.35 - 4.90: 84151 Nonbonded interactions: 196856 Sorted by model distance: nonbonded pdb=" OD2 ASP D 162 " pdb=" OH TYR D 216 " model vdw 2.134 3.040 nonbonded pdb=" OG SER C 9 " pdb=" OE1 GLU C 121 " model vdw 2.163 3.040 nonbonded pdb=" NH2 ARG E 126 " pdb=" OD1 ASP E 135 " model vdw 2.186 3.120 nonbonded pdb=" OD2 ASP C 81 " pdb=" NZ LYS C 101 " model vdw 2.215 3.120 nonbonded pdb=" O ASN D 286 " pdb=" NZ LYS D 290 " model vdw 2.238 3.120 ... (remaining 196851 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 5.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.000 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 57.840 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 : 0.010 0.098 22501 Z= 0.410 Angle : 0.946 12.184 30648 Z= 0.530 Chirality : 0.063 0.395 3387 Planarity : 0.007 0.084 3878 Dihedral : 15.766 176.579 8642 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.07 % Favored : 96.71 % Rotamer: Outliers : 1.98 % Allowed : 5.07 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.15), residues: 2674 helix: -1.11 (0.15), residues: 812 sheet: 0.01 (0.24), residues: 440 loop : 0.13 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP D 388 HIS 0.014 0.003 HIS A 384 PHE 0.032 0.004 PHE D 121 TYR 0.027 0.005 TYR A 360 ARG 0.084 0.009 ARG D 171 Details of bonding type rmsd hydrogen bonds : bond 0.18943 ( 921) hydrogen bonds : angle 8.12678 ( 2538) covalent geometry : bond 0.00962 (22501) covalent geometry : angle 0.94600 (30648) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 461 time to evaluate : 2.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 GLN cc_start: 0.7277 (mt0) cc_final: 0.7014 (mm110) REVERT: A 437 GLN cc_start: 0.7617 (mt0) cc_final: 0.7056 (mm110) REVERT: A 473 LYS cc_start: 0.8239 (mmmt) cc_final: 0.7839 (mmtm) REVERT: A 505 ASN cc_start: 0.8055 (t0) cc_final: 0.7248 (m110) REVERT: A 527 GLN cc_start: 0.8672 (tp40) cc_final: 0.8318 (tp40) REVERT: A 540 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8472 (mtp180) REVERT: A 709 LYS cc_start: 0.7632 (mtpp) cc_final: 0.7413 (mtmt) REVERT: A 714 SER cc_start: 0.8181 (t) cc_final: 0.7917 (t) REVERT: B 44 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8277 (mttt) REVERT: B 51 ASP cc_start: 0.6739 (m-30) cc_final: 0.6521 (m-30) REVERT: B 101 ASP cc_start: 0.7383 (t0) cc_final: 0.6930 (p0) REVERT: C 52 TYR cc_start: 0.7404 (t80) cc_final: 0.7190 (t80) REVERT: C 342 VAL cc_start: 0.8258 (m) cc_final: 0.8023 (t) REVERT: C 478 LYS cc_start: 0.6245 (mmpt) cc_final: 0.6022 (mmtm) REVERT: D 135 LYS cc_start: 0.8085 (tttm) cc_final: 0.7740 (mmtt) REVERT: D 177 LYS cc_start: 0.8255 (tttm) cc_final: 0.8038 (tmtt) REVERT: D 256 SER cc_start: 0.8228 (p) cc_final: 0.7892 (m) REVERT: D 422 ASN cc_start: 0.7994 (m-40) cc_final: 0.7694 (m-40) REVERT: D 467 GLN cc_start: 0.8334 (tt0) cc_final: 0.8088 (tt0) REVERT: E 555 ASP cc_start: 0.7634 (m-30) cc_final: 0.7347 (m-30) REVERT: E 571 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8127 (tppt) REVERT: E 699 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6683 (mp0) outliers start: 45 outliers final: 11 residues processed: 498 average time/residue: 1.4485 time to fit residues: 809.8221 Evaluate side-chains 297 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 282 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 ARG Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 571 LYS Chi-restraints excluded: chain E residue 699 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 227 optimal weight: 0.0020 chunk 203 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 210 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 246 HIS A 352 GLN A 642 ASN A 712 ASN A 749 ASN B 16 GLN B 120 GLN ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 GLN D 286 ASN D 355 ASN E 244 ASN E 262 ASN E 743 GLN E 788 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.128517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.104319 restraints weight = 29272.175| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.95 r_work: 0.3183 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22501 Z= 0.156 Angle : 0.624 9.309 30648 Z= 0.335 Chirality : 0.045 0.198 3387 Planarity : 0.004 0.052 3878 Dihedral : 12.934 176.599 3503 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.50 % Favored : 98.47 % Rotamer: Outliers : 2.91 % Allowed : 11.50 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.16), residues: 2674 helix: 0.75 (0.17), residues: 837 sheet: 0.05 (0.24), residues: 421 loop : 0.43 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 532 HIS 0.006 0.001 HIS B 15 PHE 0.017 0.002 PHE E 633 TYR 0.015 0.002 TYR A 283 ARG 0.006 0.001 ARG A 443 Details of bonding type rmsd hydrogen bonds : bond 0.04735 ( 921) hydrogen bonds : angle 5.88174 ( 2538) covalent geometry : bond 0.00325 (22501) covalent geometry : angle 0.62359 (30648) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 303 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.6223 (mmp-170) cc_final: 0.5783 (tpp-160) REVERT: A 155 THR cc_start: 0.9016 (t) cc_final: 0.8671 (m) REVERT: A 242 GLN cc_start: 0.7279 (mt0) cc_final: 0.6991 (mm110) REVERT: A 437 GLN cc_start: 0.7816 (mt0) cc_final: 0.7176 (mm-40) REVERT: A 456 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7832 (mm-30) REVERT: A 469 THR cc_start: 0.8431 (m) cc_final: 0.8006 (p) REVERT: A 473 LYS cc_start: 0.8217 (mmmt) cc_final: 0.7610 (mmtm) REVERT: A 505 ASN cc_start: 0.8030 (t0) cc_final: 0.7184 (m110) REVERT: A 527 GLN cc_start: 0.8866 (tp40) cc_final: 0.8660 (tp40) REVERT: A 651 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7381 (mtm180) REVERT: A 655 GLU cc_start: 0.7932 (tt0) cc_final: 0.7731 (tt0) REVERT: A 705 ASN cc_start: 0.7430 (p0) cc_final: 0.7103 (p0) REVERT: A 709 LYS cc_start: 0.7417 (mtpp) cc_final: 0.7085 (mttt) REVERT: A 714 SER cc_start: 0.7879 (t) cc_final: 0.7364 (p) REVERT: B 51 ASP cc_start: 0.7196 (m-30) cc_final: 0.6873 (m-30) REVERT: B 101 ASP cc_start: 0.6790 (t0) cc_final: 0.6096 (p0) REVERT: B 171 ILE cc_start: 0.8138 (mt) cc_final: 0.7705 (mm) REVERT: C 59 ASN cc_start: 0.5244 (t0) cc_final: 0.4914 (t0) REVERT: C 142 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.7022 (ttpp) REVERT: C 183 TYR cc_start: 0.7710 (m-80) cc_final: 0.7301 (m-80) REVERT: C 244 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6426 (mp) REVERT: C 417 ASP cc_start: 0.7884 (p0) cc_final: 0.7569 (p0) REVERT: C 478 LYS cc_start: 0.5916 (mmpt) cc_final: 0.5610 (mmtt) REVERT: C 522 GLU cc_start: 0.6801 (mp0) cc_final: 0.6485 (mp0) REVERT: D 4 LYS cc_start: 0.8336 (tptp) cc_final: 0.7851 (tmtm) REVERT: D 59 MET cc_start: 0.8824 (mtp) cc_final: 0.8614 (ttm) REVERT: D 135 LYS cc_start: 0.8331 (tttm) cc_final: 0.7608 (mmtt) REVERT: D 177 LYS cc_start: 0.8654 (tttm) cc_final: 0.8385 (ttpp) REVERT: D 253 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7228 (mm-40) REVERT: D 422 ASN cc_start: 0.7755 (m-40) cc_final: 0.7493 (m110) REVERT: E 300 GLU cc_start: 0.7894 (tt0) cc_final: 0.7692 (tt0) REVERT: E 546 LYS cc_start: 0.8320 (mtmm) cc_final: 0.8108 (mppt) REVERT: E 555 ASP cc_start: 0.8095 (m-30) cc_final: 0.7878 (m-30) outliers start: 66 outliers final: 24 residues processed: 343 average time/residue: 1.5350 time to fit residues: 591.7594 Evaluate side-chains 286 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 258 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 651 ARG Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 518 GLN Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 432 CYS Chi-restraints excluded: chain E residue 511 ASP Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 630 GLU Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain E residue 680 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 5 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 257 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 258 optimal weight: 0.7980 chunk 228 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 352 GLN A 411 GLN A 625 GLN B 120 GLN B 134 ASN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 HIS E 244 ASN E 731 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.125184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.100654 restraints weight = 29498.178| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.20 r_work: 0.3109 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22501 Z= 0.236 Angle : 0.663 10.754 30648 Z= 0.351 Chirality : 0.047 0.231 3387 Planarity : 0.005 0.072 3878 Dihedral : 12.615 178.375 3483 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.13 % Allowed : 13.57 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.16), residues: 2674 helix: 0.86 (0.18), residues: 838 sheet: -0.12 (0.23), residues: 443 loop : 0.43 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 14 HIS 0.006 0.001 HIS A 69 PHE 0.018 0.002 PHE C 326 TYR 0.016 0.002 TYR E 753 ARG 0.007 0.001 ARG C 352 Details of bonding type rmsd hydrogen bonds : bond 0.04934 ( 921) hydrogen bonds : angle 5.84207 ( 2538) covalent geometry : bond 0.00541 (22501) covalent geometry : angle 0.66313 (30648) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 280 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 THR cc_start: 0.9014 (t) cc_final: 0.8670 (m) REVERT: A 242 GLN cc_start: 0.7538 (mt0) cc_final: 0.7001 (mm110) REVERT: A 253 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8543 (tmtm) REVERT: A 437 GLN cc_start: 0.7846 (mt0) cc_final: 0.7192 (mm-40) REVERT: A 456 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7882 (mm-30) REVERT: A 469 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8016 (p) REVERT: A 473 LYS cc_start: 0.8228 (mmmt) cc_final: 0.7579 (mmtm) REVERT: A 505 ASN cc_start: 0.8026 (t0) cc_final: 0.7302 (m-40) REVERT: A 625 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.8020 (tm130) REVERT: A 651 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7522 (mtm180) REVERT: A 709 LYS cc_start: 0.7422 (mtpp) cc_final: 0.7138 (mtmt) REVERT: A 714 SER cc_start: 0.7918 (t) cc_final: 0.7478 (p) REVERT: A 765 ASP cc_start: 0.7705 (m-30) cc_final: 0.7457 (m-30) REVERT: B 51 ASP cc_start: 0.7198 (m-30) cc_final: 0.6884 (m-30) REVERT: B 101 ASP cc_start: 0.6689 (t0) cc_final: 0.6096 (p0) REVERT: B 145 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8260 (ttt180) REVERT: B 171 ILE cc_start: 0.8157 (mt) cc_final: 0.7742 (mm) REVERT: C 50 ASN cc_start: 0.6663 (p0) cc_final: 0.6452 (p0) REVERT: C 59 ASN cc_start: 0.5148 (t0) cc_final: 0.4775 (t0) REVERT: C 183 TYR cc_start: 0.7719 (m-80) cc_final: 0.7251 (m-80) REVERT: C 244 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6692 (mp) REVERT: C 417 ASP cc_start: 0.7916 (p0) cc_final: 0.7627 (p0) REVERT: C 478 LYS cc_start: 0.5986 (mmpt) cc_final: 0.5610 (mmtt) REVERT: C 522 GLU cc_start: 0.6731 (mp0) cc_final: 0.6462 (mp0) REVERT: D 1 MET cc_start: 0.2613 (OUTLIER) cc_final: 0.2039 (ppp) REVERT: D 4 LYS cc_start: 0.8360 (tptp) cc_final: 0.7903 (tmtm) REVERT: D 59 MET cc_start: 0.8914 (mtp) cc_final: 0.8697 (ttm) REVERT: D 135 LYS cc_start: 0.8440 (tttm) cc_final: 0.7696 (mmtt) REVERT: D 177 LYS cc_start: 0.8730 (tttm) cc_final: 0.8489 (ttpp) REVERT: D 253 GLN cc_start: 0.7872 (mm-40) cc_final: 0.7191 (mm-40) REVERT: D 351 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8238 (mt-10) REVERT: E 253 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7796 (pmt170) REVERT: E 555 ASP cc_start: 0.8182 (m-30) cc_final: 0.7962 (m-30) REVERT: E 571 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8049 (tttt) outliers start: 71 outliers final: 28 residues processed: 321 average time/residue: 1.5493 time to fit residues: 559.1909 Evaluate side-chains 296 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 257 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 651 ARG Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 510 ARG Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 244 ASN Chi-restraints excluded: chain E residue 253 ARG Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 511 ASP Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 571 LYS Chi-restraints excluded: chain E residue 630 GLU Chi-restraints excluded: chain E residue 676 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 51 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 197 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 219 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 352 GLN ** B 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN B 120 GLN B 134 ASN C 13 HIS ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 ASN E 244 ASN E 442 GLN E 731 GLN E 748 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.124272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.099669 restraints weight = 29398.747| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.11 r_work: 0.3099 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 22501 Z= 0.270 Angle : 0.672 9.510 30648 Z= 0.354 Chirality : 0.048 0.226 3387 Planarity : 0.006 0.076 3878 Dihedral : 12.617 179.214 3483 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.61 % Allowed : 13.96 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 2674 helix: 0.91 (0.18), residues: 823 sheet: -0.22 (0.23), residues: 441 loop : 0.28 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 58 HIS 0.006 0.001 HIS A 69 PHE 0.019 0.002 PHE E 734 TYR 0.017 0.002 TYR A 360 ARG 0.008 0.001 ARG C 352 Details of bonding type rmsd hydrogen bonds : bond 0.04886 ( 921) hydrogen bonds : angle 5.85211 ( 2538) covalent geometry : bond 0.00623 (22501) covalent geometry : angle 0.67155 (30648) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 264 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6996 (mm-30) REVERT: A 155 THR cc_start: 0.9013 (t) cc_final: 0.8679 (m) REVERT: A 242 GLN cc_start: 0.7518 (mt0) cc_final: 0.7020 (mm110) REVERT: A 253 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8541 (tmtm) REVERT: A 354 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7570 (ptmm) REVERT: A 437 GLN cc_start: 0.7873 (mt0) cc_final: 0.7192 (mm110) REVERT: A 456 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7858 (mm-30) REVERT: A 469 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.7986 (p) REVERT: A 473 LYS cc_start: 0.8211 (mmmt) cc_final: 0.7556 (mmtm) REVERT: A 505 ASN cc_start: 0.8131 (t0) cc_final: 0.7362 (m-40) REVERT: A 564 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7792 (mp0) REVERT: A 651 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7523 (mtm180) REVERT: A 655 GLU cc_start: 0.7995 (tt0) cc_final: 0.7724 (tt0) REVERT: A 709 LYS cc_start: 0.7450 (mtpp) cc_final: 0.7140 (mtmm) REVERT: A 714 SER cc_start: 0.7869 (t) cc_final: 0.7362 (p) REVERT: B 15 HIS cc_start: 0.8405 (m170) cc_final: 0.8191 (m90) REVERT: B 51 ASP cc_start: 0.7190 (m-30) cc_final: 0.6888 (m-30) REVERT: B 101 ASP cc_start: 0.6695 (t0) cc_final: 0.6109 (p0) REVERT: B 145 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8275 (ttt180) REVERT: B 158 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7854 (mmmt) REVERT: B 171 ILE cc_start: 0.8225 (mt) cc_final: 0.7846 (mm) REVERT: C 45 ARG cc_start: 0.7631 (mtm-85) cc_final: 0.7413 (mtm180) REVERT: C 59 ASN cc_start: 0.5109 (t0) cc_final: 0.4707 (t0) REVERT: C 183 TYR cc_start: 0.7733 (m-80) cc_final: 0.7306 (m-80) REVERT: C 244 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6739 (mp) REVERT: C 417 ASP cc_start: 0.7932 (p0) cc_final: 0.7657 (p0) REVERT: C 478 LYS cc_start: 0.6016 (mmpt) cc_final: 0.5630 (mmtt) REVERT: D 1 MET cc_start: 0.2907 (tmm) cc_final: 0.2341 (ppp) REVERT: D 4 LYS cc_start: 0.8403 (tptp) cc_final: 0.7964 (tmtm) REVERT: D 59 MET cc_start: 0.8928 (mtp) cc_final: 0.8717 (mtm) REVERT: D 135 LYS cc_start: 0.8414 (tttm) cc_final: 0.7700 (mmtt) REVERT: D 177 LYS cc_start: 0.8713 (tttm) cc_final: 0.8471 (ttpp) REVERT: D 253 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7200 (mm-40) REVERT: D 256 SER cc_start: 0.8269 (p) cc_final: 0.8015 (m) REVERT: D 351 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8209 (mt-10) REVERT: E 235 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8529 (mmt) REVERT: E 253 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7859 (pmt170) REVERT: E 288 MET cc_start: 0.6014 (tpp) cc_final: 0.5809 (tpp) REVERT: E 555 ASP cc_start: 0.8190 (m-30) cc_final: 0.7951 (m-30) REVERT: E 700 THR cc_start: 0.8280 (m) cc_final: 0.8000 (p) outliers start: 82 outliers final: 36 residues processed: 319 average time/residue: 1.5532 time to fit residues: 556.0711 Evaluate side-chains 302 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 255 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 651 ARG Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 510 ARG Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 235 MET Chi-restraints excluded: chain E residue 253 ARG Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 630 GLU Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain E residue 710 SER Chi-restraints excluded: chain E residue 748 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 198 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 173 optimal weight: 0.7980 chunk 168 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 238 ASN A 352 GLN A 625 GLN ** B 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN B 134 ASN ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 ASN E 244 ASN E 494 ASN E 519 ASN E 731 GLN E 748 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.126665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.102398 restraints weight = 29303.907| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.08 r_work: 0.3143 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22501 Z= 0.150 Angle : 0.573 8.665 30648 Z= 0.304 Chirality : 0.043 0.206 3387 Planarity : 0.004 0.049 3878 Dihedral : 12.384 177.798 3483 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.86 % Allowed : 15.07 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.16), residues: 2674 helix: 1.19 (0.18), residues: 829 sheet: -0.18 (0.24), residues: 416 loop : 0.34 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 532 HIS 0.004 0.001 HIS A 69 PHE 0.015 0.002 PHE E 734 TYR 0.015 0.001 TYR A 283 ARG 0.009 0.000 ARG C 352 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 921) hydrogen bonds : angle 5.58144 ( 2538) covalent geometry : bond 0.00334 (22501) covalent geometry : angle 0.57346 (30648) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 270 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.6336 (mmp-170) cc_final: 0.5981 (tpp-160) REVERT: A 160 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8131 (mm) REVERT: A 242 GLN cc_start: 0.7519 (mt0) cc_final: 0.7054 (mm110) REVERT: A 354 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7633 (ptmm) REVERT: A 437 GLN cc_start: 0.7898 (mt0) cc_final: 0.7280 (mm-40) REVERT: A 456 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7844 (mm-30) REVERT: A 469 THR cc_start: 0.8467 (m) cc_final: 0.8079 (p) REVERT: A 473 LYS cc_start: 0.8293 (mmmt) cc_final: 0.7652 (mmtm) REVERT: A 505 ASN cc_start: 0.8087 (t0) cc_final: 0.7417 (m-40) REVERT: A 564 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7783 (mp0) REVERT: A 651 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7568 (mtm180) REVERT: A 655 GLU cc_start: 0.7963 (tt0) cc_final: 0.7739 (tt0) REVERT: A 709 LYS cc_start: 0.7457 (mtpp) cc_final: 0.7165 (mtmm) REVERT: A 714 SER cc_start: 0.7954 (t) cc_final: 0.7562 (p) REVERT: A 765 ASP cc_start: 0.7711 (m-30) cc_final: 0.7504 (m-30) REVERT: B 51 ASP cc_start: 0.7201 (m-30) cc_final: 0.6923 (m-30) REVERT: B 101 ASP cc_start: 0.6525 (t0) cc_final: 0.5988 (p0) REVERT: B 145 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8188 (ttt180) REVERT: B 171 ILE cc_start: 0.8269 (mt) cc_final: 0.7951 (mm) REVERT: C 49 THR cc_start: 0.6219 (OUTLIER) cc_final: 0.5939 (p) REVERT: C 54 GLN cc_start: 0.7413 (tp40) cc_final: 0.7017 (mt0) REVERT: C 59 ASN cc_start: 0.5027 (t0) cc_final: 0.4630 (t0) REVERT: C 146 LYS cc_start: 0.7961 (ptmm) cc_final: 0.7681 (ttpt) REVERT: C 183 TYR cc_start: 0.7780 (m-80) cc_final: 0.7423 (m-80) REVERT: C 244 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6839 (mp) REVERT: C 309 ASP cc_start: 0.7435 (t0) cc_final: 0.7165 (t0) REVERT: C 417 ASP cc_start: 0.7918 (p0) cc_final: 0.7672 (p0) REVERT: C 478 LYS cc_start: 0.5960 (mmpt) cc_final: 0.5653 (mmtt) REVERT: C 512 LYS cc_start: 0.8142 (mmmt) cc_final: 0.7063 (mmtm) REVERT: D 1 MET cc_start: 0.2630 (OUTLIER) cc_final: 0.2054 (pp-130) REVERT: D 4 LYS cc_start: 0.8387 (tptp) cc_final: 0.8026 (tmtm) REVERT: D 59 MET cc_start: 0.8940 (mtp) cc_final: 0.8704 (ttm) REVERT: D 135 LYS cc_start: 0.8420 (tttm) cc_final: 0.7772 (mmtt) REVERT: D 177 LYS cc_start: 0.8744 (tttm) cc_final: 0.8535 (ttpp) REVERT: D 256 SER cc_start: 0.8283 (p) cc_final: 0.8058 (m) REVERT: D 351 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8181 (mt-10) REVERT: E 300 GLU cc_start: 0.7876 (tt0) cc_final: 0.7626 (tt0) REVERT: E 313 ARG cc_start: 0.7005 (mmm160) cc_final: 0.6604 (mmm160) REVERT: E 381 ARG cc_start: 0.8109 (ttm110) cc_final: 0.7885 (ttp-110) REVERT: E 555 ASP cc_start: 0.8184 (m-30) cc_final: 0.7946 (m-30) outliers start: 65 outliers final: 30 residues processed: 309 average time/residue: 1.4782 time to fit residues: 514.8555 Evaluate side-chains 290 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 251 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 651 ARG Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 562 ASP Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 622 LYS Chi-restraints excluded: chain E residue 630 GLU Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain E residue 748 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 19 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 189 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 238 ASN A 352 GLN A 625 GLN B 16 GLN B 43 GLN B 112 GLN B 120 GLN B 134 ASN C 112 GLN ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.123748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.099326 restraints weight = 29179.246| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.06 r_work: 0.3090 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 22501 Z= 0.315 Angle : 0.702 10.212 30648 Z= 0.369 Chirality : 0.049 0.238 3387 Planarity : 0.006 0.088 3878 Dihedral : 12.622 179.298 3482 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.39 % Allowed : 14.98 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.16), residues: 2674 helix: 0.89 (0.18), residues: 832 sheet: -0.33 (0.23), residues: 444 loop : 0.23 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP D 343 HIS 0.006 0.001 HIS A 69 PHE 0.020 0.003 PHE E 734 TYR 0.020 0.002 TYR A 360 ARG 0.009 0.001 ARG C 352 Details of bonding type rmsd hydrogen bonds : bond 0.05009 ( 921) hydrogen bonds : angle 5.88919 ( 2538) covalent geometry : bond 0.00728 (22501) covalent geometry : angle 0.70181 (30648) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 262 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7087 (mm-30) REVERT: A 242 GLN cc_start: 0.7540 (mt0) cc_final: 0.7062 (mm110) REVERT: A 354 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7650 (ptmm) REVERT: A 437 GLN cc_start: 0.7880 (mt0) cc_final: 0.7253 (mm110) REVERT: A 456 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7896 (mm-30) REVERT: A 469 THR cc_start: 0.8468 (m) cc_final: 0.8051 (p) REVERT: A 473 LYS cc_start: 0.8290 (mmmt) cc_final: 0.7633 (mmtm) REVERT: A 505 ASN cc_start: 0.8113 (t0) cc_final: 0.7424 (m-40) REVERT: A 564 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7805 (mp0) REVERT: A 625 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7999 (tm130) REVERT: A 651 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7623 (mtm180) REVERT: A 655 GLU cc_start: 0.8052 (tt0) cc_final: 0.7838 (tt0) REVERT: A 709 LYS cc_start: 0.7495 (mtpp) cc_final: 0.7162 (mtmm) REVERT: A 714 SER cc_start: 0.7966 (t) cc_final: 0.7514 (p) REVERT: B 16 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: B 51 ASP cc_start: 0.7184 (m-30) cc_final: 0.6907 (m-30) REVERT: B 101 ASP cc_start: 0.6863 (t0) cc_final: 0.6250 (p0) REVERT: B 145 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8298 (ttt180) REVERT: B 158 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7929 (mmmt) REVERT: C 49 THR cc_start: 0.6272 (OUTLIER) cc_final: 0.5939 (p) REVERT: C 59 ASN cc_start: 0.5063 (t0) cc_final: 0.4613 (t0) REVERT: C 142 LYS cc_start: 0.7618 (ttpp) cc_final: 0.7412 (ttpp) REVERT: C 183 TYR cc_start: 0.7790 (m-80) cc_final: 0.7427 (m-80) REVERT: C 244 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6762 (mp) REVERT: C 252 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7677 (pm20) REVERT: C 309 ASP cc_start: 0.7439 (t0) cc_final: 0.7218 (t0) REVERT: C 417 ASP cc_start: 0.7971 (p0) cc_final: 0.7723 (p0) REVERT: C 478 LYS cc_start: 0.6144 (mmpt) cc_final: 0.5745 (mmtt) REVERT: C 512 LYS cc_start: 0.8207 (mmmt) cc_final: 0.7130 (mmtm) REVERT: D 4 LYS cc_start: 0.8418 (tptp) cc_final: 0.8050 (tmtm) REVERT: D 135 LYS cc_start: 0.8452 (tttm) cc_final: 0.7784 (mmtt) REVERT: D 177 LYS cc_start: 0.8762 (tttm) cc_final: 0.8559 (ttpp) REVERT: D 253 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7199 (mm-40) REVERT: D 256 SER cc_start: 0.8323 (p) cc_final: 0.8049 (m) REVERT: D 351 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8227 (mt-10) REVERT: E 397 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7544 (mt-10) REVERT: E 519 ASN cc_start: 0.7671 (t0) cc_final: 0.7437 (t0) REVERT: E 555 ASP cc_start: 0.8170 (m-30) cc_final: 0.7931 (m-30) REVERT: E 700 THR cc_start: 0.8364 (m) cc_final: 0.8081 (p) outliers start: 77 outliers final: 45 residues processed: 315 average time/residue: 1.5691 time to fit residues: 557.9979 Evaluate side-chains 306 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 249 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 651 ARG Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 562 ASP Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 630 GLU Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain E residue 709 ILE Chi-restraints excluded: chain E residue 710 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 14 optimal weight: 0.9980 chunk 247 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 257 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 250 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A 352 GLN ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN B 134 ASN C 12 GLN C 13 HIS ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 ASN E 519 ASN E 748 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.126472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.102151 restraints weight = 29221.798| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.10 r_work: 0.3139 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22501 Z= 0.153 Angle : 0.580 8.612 30648 Z= 0.308 Chirality : 0.043 0.233 3387 Planarity : 0.005 0.050 3878 Dihedral : 12.387 177.955 3482 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.73 % Allowed : 15.81 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.16), residues: 2674 helix: 1.16 (0.18), residues: 835 sheet: -0.26 (0.24), residues: 431 loop : 0.32 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 532 HIS 0.003 0.001 HIS D 382 PHE 0.014 0.002 PHE E 734 TYR 0.015 0.001 TYR A 283 ARG 0.010 0.000 ARG C 352 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 921) hydrogen bonds : angle 5.58809 ( 2538) covalent geometry : bond 0.00341 (22501) covalent geometry : angle 0.57991 (30648) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 255 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 GLN cc_start: 0.7540 (mt0) cc_final: 0.7120 (mm110) REVERT: A 354 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7617 (ptmm) REVERT: A 437 GLN cc_start: 0.7893 (mt0) cc_final: 0.7277 (mm110) REVERT: A 456 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7819 (mm-30) REVERT: A 469 THR cc_start: 0.8450 (m) cc_final: 0.8063 (p) REVERT: A 473 LYS cc_start: 0.8302 (mmmt) cc_final: 0.7678 (mmtm) REVERT: A 505 ASN cc_start: 0.8079 (t0) cc_final: 0.7422 (m-40) REVERT: A 564 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7806 (mp0) REVERT: A 651 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7524 (mtm180) REVERT: A 705 ASN cc_start: 0.7278 (p0) cc_final: 0.7028 (p0) REVERT: A 709 LYS cc_start: 0.7488 (mtpp) cc_final: 0.7162 (mtmm) REVERT: A 714 SER cc_start: 0.7940 (t) cc_final: 0.7581 (p) REVERT: A 745 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.7010 (tt0) REVERT: B 51 ASP cc_start: 0.7178 (m-30) cc_final: 0.6918 (m-30) REVERT: B 62 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.6974 (mmm160) REVERT: B 101 ASP cc_start: 0.6563 (t0) cc_final: 0.6045 (p0) REVERT: B 145 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8167 (ttt180) REVERT: B 171 ILE cc_start: 0.8257 (mt) cc_final: 0.7986 (mt) REVERT: C 49 THR cc_start: 0.6165 (OUTLIER) cc_final: 0.5884 (p) REVERT: C 54 GLN cc_start: 0.7225 (tp40) cc_final: 0.6924 (mt0) REVERT: C 59 ASN cc_start: 0.4765 (t0) cc_final: 0.4399 (t0) REVERT: C 142 LYS cc_start: 0.7597 (ttpp) cc_final: 0.7394 (ttpp) REVERT: C 183 TYR cc_start: 0.7784 (m-80) cc_final: 0.7484 (m-80) REVERT: C 244 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6831 (mp) REVERT: C 309 ASP cc_start: 0.7424 (t0) cc_final: 0.7206 (t0) REVERT: C 417 ASP cc_start: 0.7873 (p0) cc_final: 0.7628 (p0) REVERT: C 478 LYS cc_start: 0.6062 (mmpt) cc_final: 0.5726 (mmtt) REVERT: C 512 LYS cc_start: 0.8151 (mmmt) cc_final: 0.7119 (mmtm) REVERT: D 4 LYS cc_start: 0.8378 (tptp) cc_final: 0.8020 (tmtm) REVERT: D 59 MET cc_start: 0.8944 (mtp) cc_final: 0.8709 (ttm) REVERT: D 135 LYS cc_start: 0.8416 (tttm) cc_final: 0.7746 (mmtt) REVERT: D 177 LYS cc_start: 0.8733 (tttm) cc_final: 0.8520 (ttpp) REVERT: D 256 SER cc_start: 0.8320 (p) cc_final: 0.8076 (m) REVERT: D 351 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8203 (mt-10) REVERT: D 427 LYS cc_start: 0.7949 (pttm) cc_final: 0.7714 (pmtt) REVERT: E 468 GLU cc_start: 0.7825 (tp30) cc_final: 0.7547 (tp30) REVERT: E 555 ASP cc_start: 0.8133 (m-30) cc_final: 0.7892 (m-30) REVERT: E 700 THR cc_start: 0.8291 (m) cc_final: 0.7995 (p) outliers start: 62 outliers final: 37 residues processed: 292 average time/residue: 1.4247 time to fit residues: 471.2189 Evaluate side-chains 293 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 247 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 651 ARG Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 745 GLN Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 630 GLU Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain E residue 710 SER Chi-restraints excluded: chain E residue 748 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 214 optimal weight: 0.9980 chunk 151 optimal weight: 0.5980 chunk 149 optimal weight: 0.9980 chunk 172 optimal weight: 0.2980 chunk 200 optimal weight: 0.0770 chunk 168 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 226 optimal weight: 0.9980 chunk 197 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 213 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A 352 GLN ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN B 134 ASN C 12 GLN ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN E 519 ASN E 748 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.127616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.103781 restraints weight = 29450.256| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.02 r_work: 0.3171 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22501 Z= 0.124 Angle : 0.547 12.118 30648 Z= 0.291 Chirality : 0.042 0.221 3387 Planarity : 0.004 0.049 3878 Dihedral : 12.203 178.004 3481 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.91 % Favored : 98.06 % Rotamer: Outliers : 2.20 % Allowed : 16.78 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.16), residues: 2674 helix: 1.40 (0.18), residues: 829 sheet: -0.27 (0.24), residues: 429 loop : 0.42 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 532 HIS 0.004 0.001 HIS B 15 PHE 0.013 0.001 PHE E 734 TYR 0.015 0.001 TYR A 283 ARG 0.011 0.000 ARG E 259 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 921) hydrogen bonds : angle 5.39766 ( 2538) covalent geometry : bond 0.00274 (22501) covalent geometry : angle 0.54738 (30648) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 267 time to evaluate : 2.411 Fit side-chains revert: symmetry clash REVERT: A 65 ARG cc_start: 0.6250 (mmp-170) cc_final: 0.5763 (tpp-160) REVERT: A 242 GLN cc_start: 0.7493 (mt0) cc_final: 0.6987 (mm110) REVERT: A 354 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7532 (ptmm) REVERT: A 437 GLN cc_start: 0.7832 (mt0) cc_final: 0.7237 (mm-40) REVERT: A 456 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7809 (mm-30) REVERT: A 469 THR cc_start: 0.8362 (m) cc_final: 0.8083 (t) REVERT: A 473 LYS cc_start: 0.8251 (mmmt) cc_final: 0.7592 (mmtm) REVERT: A 505 ASN cc_start: 0.8028 (t0) cc_final: 0.7316 (m-40) REVERT: A 564 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7778 (mp0) REVERT: A 651 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7409 (mtm180) REVERT: A 671 MET cc_start: 0.7849 (tpt) cc_final: 0.7638 (tpp) REVERT: A 705 ASN cc_start: 0.7162 (p0) cc_final: 0.6884 (p0) REVERT: A 709 LYS cc_start: 0.7434 (mtpp) cc_final: 0.7150 (mtmm) REVERT: A 714 SER cc_start: 0.7784 (t) cc_final: 0.7553 (p) REVERT: B 51 ASP cc_start: 0.7225 (m-30) cc_final: 0.6987 (m-30) REVERT: B 87 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7427 (mm-30) REVERT: B 101 ASP cc_start: 0.6402 (t0) cc_final: 0.5881 (p0) REVERT: B 111 LEU cc_start: 0.8439 (pp) cc_final: 0.8208 (pt) REVERT: C 49 THR cc_start: 0.6068 (OUTLIER) cc_final: 0.5817 (p) REVERT: C 54 GLN cc_start: 0.7099 (tp40) cc_final: 0.6840 (mt0) REVERT: C 59 ASN cc_start: 0.4848 (t0) cc_final: 0.4473 (t0) REVERT: C 86 LEU cc_start: 0.8552 (tt) cc_final: 0.8300 (tp) REVERT: C 108 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7492 (tp30) REVERT: C 142 LYS cc_start: 0.7521 (ttpp) cc_final: 0.7302 (ttpp) REVERT: C 183 TYR cc_start: 0.7710 (m-80) cc_final: 0.7447 (m-80) REVERT: C 229 ASP cc_start: 0.8086 (p0) cc_final: 0.7857 (m-30) REVERT: C 244 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6755 (mp) REVERT: C 309 ASP cc_start: 0.7369 (t0) cc_final: 0.7122 (t70) REVERT: C 417 ASP cc_start: 0.7784 (p0) cc_final: 0.7508 (p0) REVERT: C 478 LYS cc_start: 0.5917 (mmpt) cc_final: 0.5578 (mmtt) REVERT: C 512 LYS cc_start: 0.8054 (mmmt) cc_final: 0.6997 (mmtm) REVERT: D 4 LYS cc_start: 0.8363 (tptp) cc_final: 0.7956 (tmtm) REVERT: D 59 MET cc_start: 0.8935 (mtp) cc_final: 0.8712 (ttm) REVERT: D 177 LYS cc_start: 0.8692 (tttm) cc_final: 0.8426 (ttpp) REVERT: D 427 LYS cc_start: 0.7861 (pttm) cc_final: 0.7604 (pmtt) REVERT: E 317 ARG cc_start: 0.6895 (mmt180) cc_final: 0.6585 (mmt180) REVERT: E 555 ASP cc_start: 0.8129 (m-30) cc_final: 0.7908 (m-30) REVERT: E 700 THR cc_start: 0.8195 (m) cc_final: 0.7867 (p) outliers start: 50 outliers final: 27 residues processed: 299 average time/residue: 1.3841 time to fit residues: 471.9461 Evaluate side-chains 287 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 254 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 651 ARG Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 562 ASP Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain E residue 710 SER Chi-restraints excluded: chain E residue 748 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 54 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 249 optimal weight: 3.9990 chunk 213 optimal weight: 0.3980 chunk 202 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A 352 GLN ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN B 120 GLN B 134 ASN C 12 GLN ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN E 494 ASN E 519 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.124434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.097833 restraints weight = 29699.761| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.61 r_work: 0.3150 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 22501 Z= 0.244 Angle : 0.641 11.681 30648 Z= 0.336 Chirality : 0.047 0.214 3387 Planarity : 0.005 0.072 3878 Dihedral : 12.388 177.589 3480 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.02 % Favored : 97.94 % Rotamer: Outliers : 2.38 % Allowed : 16.96 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.16), residues: 2674 helix: 1.18 (0.18), residues: 826 sheet: -0.29 (0.23), residues: 440 loop : 0.34 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 343 HIS 0.006 0.001 HIS A 69 PHE 0.019 0.002 PHE E 734 TYR 0.017 0.002 TYR A 360 ARG 0.017 0.001 ARG E 259 Details of bonding type rmsd hydrogen bonds : bond 0.04503 ( 921) hydrogen bonds : angle 5.65416 ( 2538) covalent geometry : bond 0.00562 (22501) covalent geometry : angle 0.64081 (30648) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 251 time to evaluate : 2.403 Fit side-chains revert: symmetry clash REVERT: A 242 GLN cc_start: 0.7519 (mt0) cc_final: 0.7089 (mm110) REVERT: A 286 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7841 (ttpt) REVERT: A 354 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7535 (ptmm) REVERT: A 389 ASP cc_start: 0.7866 (m-30) cc_final: 0.7650 (m-30) REVERT: A 437 GLN cc_start: 0.7901 (mt0) cc_final: 0.7263 (mm110) REVERT: A 456 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7730 (mm-30) REVERT: A 469 THR cc_start: 0.8365 (m) cc_final: 0.7972 (p) REVERT: A 473 LYS cc_start: 0.8245 (mmmt) cc_final: 0.7602 (mmtm) REVERT: A 505 ASN cc_start: 0.8045 (t0) cc_final: 0.7352 (m-40) REVERT: A 564 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7761 (mp0) REVERT: A 651 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7466 (mtm180) REVERT: A 709 LYS cc_start: 0.7463 (mtpp) cc_final: 0.7165 (mtmm) REVERT: A 714 SER cc_start: 0.7784 (t) cc_final: 0.7501 (p) REVERT: A 745 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6988 (tt0) REVERT: B 51 ASP cc_start: 0.7123 (m-30) cc_final: 0.6889 (m-30) REVERT: B 101 ASP cc_start: 0.6411 (t0) cc_final: 0.5860 (p0) REVERT: B 158 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7960 (mmmt) REVERT: C 49 THR cc_start: 0.6185 (OUTLIER) cc_final: 0.5877 (p) REVERT: C 54 GLN cc_start: 0.7197 (tp40) cc_final: 0.6928 (mt0) REVERT: C 59 ASN cc_start: 0.4932 (t0) cc_final: 0.4510 (t0) REVERT: C 142 LYS cc_start: 0.7572 (ttpp) cc_final: 0.7335 (ttpp) REVERT: C 244 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6835 (mp) REVERT: C 309 ASP cc_start: 0.7327 (t0) cc_final: 0.7103 (t0) REVERT: C 417 ASP cc_start: 0.7769 (p0) cc_final: 0.7516 (p0) REVERT: C 478 LYS cc_start: 0.6013 (mmpt) cc_final: 0.5675 (mmtt) REVERT: C 512 LYS cc_start: 0.8120 (mmmt) cc_final: 0.7056 (mmtm) REVERT: D 4 LYS cc_start: 0.8317 (tptp) cc_final: 0.7908 (tmtm) REVERT: D 59 MET cc_start: 0.8936 (mtp) cc_final: 0.8692 (ttm) REVERT: D 135 LYS cc_start: 0.8361 (tttm) cc_final: 0.7510 (mmtt) REVERT: D 177 LYS cc_start: 0.8676 (tttm) cc_final: 0.8436 (ttpp) REVERT: D 256 SER cc_start: 0.8283 (p) cc_final: 0.8028 (m) REVERT: D 427 LYS cc_start: 0.7935 (pttm) cc_final: 0.7705 (pmtt) REVERT: D 512 ASP cc_start: 0.6653 (OUTLIER) cc_final: 0.6445 (p0) REVERT: E 317 ARG cc_start: 0.6888 (mmt180) cc_final: 0.6520 (mmt180) REVERT: E 468 GLU cc_start: 0.7782 (tp30) cc_final: 0.7504 (tp30) REVERT: E 555 ASP cc_start: 0.8167 (m-30) cc_final: 0.7913 (m-30) REVERT: E 700 THR cc_start: 0.8290 (m) cc_final: 0.8012 (p) outliers start: 54 outliers final: 36 residues processed: 286 average time/residue: 1.4095 time to fit residues: 456.0138 Evaluate side-chains 291 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 246 time to evaluate : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 651 ARG Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 745 GLN Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 512 ASP Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain E residue 630 GLU Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain E residue 710 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 228 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 255 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 204 optimal weight: 0.9990 chunk 257 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A 352 GLN B 43 GLN B 120 GLN B 134 ASN C 12 GLN ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 519 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.126469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.102267 restraints weight = 29458.234| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.15 r_work: 0.3143 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22501 Z= 0.147 Angle : 0.572 11.643 30648 Z= 0.302 Chirality : 0.043 0.207 3387 Planarity : 0.004 0.067 3878 Dihedral : 12.259 177.886 3480 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.83 % Favored : 98.13 % Rotamer: Outliers : 1.89 % Allowed : 17.49 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.16), residues: 2674 helix: 1.34 (0.18), residues: 827 sheet: -0.27 (0.24), residues: 430 loop : 0.40 (0.17), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 532 HIS 0.003 0.001 HIS B 15 PHE 0.014 0.002 PHE E 734 TYR 0.016 0.001 TYR A 283 ARG 0.012 0.000 ARG E 259 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 921) hydrogen bonds : angle 5.47054 ( 2538) covalent geometry : bond 0.00330 (22501) covalent geometry : angle 0.57196 (30648) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 257 time to evaluate : 2.374 Fit side-chains revert: symmetry clash REVERT: A 65 ARG cc_start: 0.6299 (mmp-170) cc_final: 0.5854 (tpp-160) REVERT: A 242 GLN cc_start: 0.7509 (mt0) cc_final: 0.7029 (mm110) REVERT: A 354 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7559 (ptmm) REVERT: A 389 ASP cc_start: 0.7835 (m-30) cc_final: 0.7594 (m-30) REVERT: A 437 GLN cc_start: 0.7914 (mt0) cc_final: 0.7238 (mm110) REVERT: A 469 THR cc_start: 0.8356 (m) cc_final: 0.7971 (p) REVERT: A 473 LYS cc_start: 0.8231 (mmmt) cc_final: 0.7598 (mmtm) REVERT: A 505 ASN cc_start: 0.8038 (t0) cc_final: 0.7328 (m-40) REVERT: A 564 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7812 (mp0) REVERT: A 651 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7456 (mtm180) REVERT: A 709 LYS cc_start: 0.7445 (mtpp) cc_final: 0.7135 (mtmm) REVERT: A 714 SER cc_start: 0.7781 (t) cc_final: 0.7537 (p) REVERT: A 745 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.7039 (tt0) REVERT: B 51 ASP cc_start: 0.7210 (m-30) cc_final: 0.6968 (m-30) REVERT: B 158 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7943 (mmmt) REVERT: C 12 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.6370 (tm130) REVERT: C 49 THR cc_start: 0.6131 (OUTLIER) cc_final: 0.5811 (p) REVERT: C 54 GLN cc_start: 0.7085 (tp40) cc_final: 0.6824 (mt0) REVERT: C 59 ASN cc_start: 0.4975 (t0) cc_final: 0.4558 (t0) REVERT: C 86 LEU cc_start: 0.8576 (tt) cc_final: 0.8333 (tp) REVERT: C 142 LYS cc_start: 0.7594 (ttpp) cc_final: 0.7363 (ttpp) REVERT: C 244 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6776 (mp) REVERT: C 309 ASP cc_start: 0.7371 (t0) cc_final: 0.7133 (t0) REVERT: C 417 ASP cc_start: 0.7790 (p0) cc_final: 0.7516 (p0) REVERT: C 478 LYS cc_start: 0.5930 (mmpt) cc_final: 0.5563 (mmtt) REVERT: C 512 LYS cc_start: 0.8063 (mmmt) cc_final: 0.6994 (mmtm) REVERT: C 533 LYS cc_start: 0.7948 (mmtp) cc_final: 0.7619 (mmtt) REVERT: D 4 LYS cc_start: 0.8343 (tptp) cc_final: 0.7952 (tmtm) REVERT: D 59 MET cc_start: 0.8961 (mtp) cc_final: 0.8724 (ttm) REVERT: D 135 LYS cc_start: 0.8404 (tttm) cc_final: 0.7530 (mmtt) REVERT: D 177 LYS cc_start: 0.8699 (tttm) cc_final: 0.8427 (ttpp) REVERT: D 256 SER cc_start: 0.8204 (p) cc_final: 0.7975 (m) REVERT: D 427 LYS cc_start: 0.7890 (pttm) cc_final: 0.7666 (pmtt) REVERT: D 512 ASP cc_start: 0.6652 (OUTLIER) cc_final: 0.6437 (p0) REVERT: E 317 ARG cc_start: 0.6880 (mmt180) cc_final: 0.6527 (mmt180) REVERT: E 468 GLU cc_start: 0.7876 (tp30) cc_final: 0.7565 (tp30) REVERT: E 555 ASP cc_start: 0.8231 (m-30) cc_final: 0.7970 (m-30) REVERT: E 594 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.6882 (tm130) REVERT: E 700 THR cc_start: 0.8279 (m) cc_final: 0.7976 (p) outliers start: 43 outliers final: 26 residues processed: 287 average time/residue: 1.4534 time to fit residues: 471.1078 Evaluate side-chains 286 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 251 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 651 ARG Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 745 GLN Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 512 ASP Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 594 GLN Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain E residue 710 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 3 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 97 optimal weight: 7.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A 352 GLN ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN B 134 ASN C 151 ASN ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN E 335 HIS E 494 ASN E 519 ASN E 731 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.126458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.102260 restraints weight = 29399.326| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.16 r_work: 0.3144 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 22501 Z= 0.163 Angle : 0.734 59.187 30648 Z= 0.412 Chirality : 0.043 0.483 3387 Planarity : 0.004 0.066 3878 Dihedral : 12.255 177.892 3480 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.76 % Favored : 98.20 % Rotamer: Outliers : 1.94 % Allowed : 17.89 % Favored : 80.18 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.16), residues: 2674 helix: 1.35 (0.18), residues: 827 sheet: -0.27 (0.24), residues: 430 loop : 0.40 (0.17), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 532 HIS 0.004 0.001 HIS B 15 PHE 0.014 0.002 PHE E 734 TYR 0.014 0.001 TYR A 283 ARG 0.009 0.000 ARG E 259 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 921) hydrogen bonds : angle 5.47098 ( 2538) covalent geometry : bond 0.00352 (22501) covalent geometry : angle 0.73429 (30648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19062.53 seconds wall clock time: 328 minutes 10.04 seconds (19690.04 seconds total)