Starting phenix.real_space_refine on Tue Aug 26 10:51:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bf5_16013/08_2025/8bf5_16013.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bf5_16013/08_2025/8bf5_16013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bf5_16013/08_2025/8bf5_16013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bf5_16013/08_2025/8bf5_16013.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bf5_16013/08_2025/8bf5_16013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bf5_16013/08_2025/8bf5_16013.map" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 7 Type Number sf(0) Gaussians P 43 5.49 5 Mg 3 5.21 5 S 131 5.16 5 C 11254 2.51 5 N 3105 2.21 5 O 3472 1.98 5 H 17699 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35707 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 11187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 11187 Classifications: {'peptide': 697} Link IDs: {'PTRANS': 26, 'TRANS': 670} Chain breaks: 1 Chain: "B" Number of atoms: 11418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 11418 Classifications: {'peptide': 726} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 692} Chain breaks: 2 Chain: "C" Number of atoms: 11827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 11827 Classifications: {'peptide': 729} Link IDs: {'PTRANS': 28, 'TRANS': 700} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "V" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 392 Classifications: {'RNA': 12} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 8} Chain: "R" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 392 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 10} Chain: "M" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 405 Classifications: {'RNA': 13} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 9} Link IDs: {'rna2p': 1, 'rna3p': 11} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'G2P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'GTA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.22, per 1000 atoms: 0.17 Number of scatterers: 35707 At special positions: 0 Unit cell: (121.929, 125.015, 115.755, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 131 16.00 P 43 15.00 Mg 3 11.99 O 3472 8.00 N 3105 7.00 C 11254 6.00 H 17699 1.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.02 Conformation dependent library (CDL) restraints added in 980.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4010 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 23 sheets defined 52.4% alpha, 13.1% beta 11 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 5.80 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 Processing helix chain 'A' and resid 10 through 24 Processing helix chain 'A' and resid 31 through 49 removed outlier: 3.540A pdb=" N LEU A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 100 Processing helix chain 'A' and resid 127 through 139 removed outlier: 3.690A pdb=" N TYR A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 184 removed outlier: 3.671A pdb=" N LYS A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 192 removed outlier: 4.182A pdb=" N VAL A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 215 removed outlier: 3.515A pdb=" N SER A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 237 through 246 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 332 through 349 Processing helix chain 'A' and resid 359 through 367 Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 401 through 412 Processing helix chain 'A' and resid 429 through 448 removed outlier: 3.570A pdb=" N TYR A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR A 448 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 472 Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.900A pdb=" N SER A 530 " --> pdb=" O ARG A 527 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLY A 531 " --> pdb=" O VAL A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 572 Processing helix chain 'A' and resid 574 through 596 removed outlier: 4.212A pdb=" N LEU A 578 " --> pdb=" O ARG A 574 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN A 583 " --> pdb=" O GLN A 579 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 605 Processing helix chain 'A' and resid 629 through 646 Processing helix chain 'A' and resid 648 through 670 removed outlier: 3.581A pdb=" N LEU A 664 " --> pdb=" O ARG A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 688 Processing helix chain 'A' and resid 693 through 719 removed outlier: 4.346A pdb=" N SER A 719 " --> pdb=" O LYS A 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 12 removed outlier: 3.967A pdb=" N ASP B 11 " --> pdb=" O PHE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 22 removed outlier: 5.478A pdb=" N SER B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 116 Processing helix chain 'B' and resid 118 through 124 Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.541A pdb=" N PHE B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 174 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 265 removed outlier: 4.433A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 292 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.253A pdb=" N ALA B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 377 through 381 Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 413 through 427 removed outlier: 3.764A pdb=" N ILE B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 472 Processing helix chain 'B' and resid 507 through 512 removed outlier: 4.243A pdb=" N GLY B 512 " --> pdb=" O PRO B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'B' and resid 539 through 559 Processing helix chain 'B' and resid 569 through 582 removed outlier: 4.302A pdb=" N ILE B 574 " --> pdb=" O LYS B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 588 Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 606 through 612 Processing helix chain 'B' and resid 616 through 624 Processing helix chain 'B' and resid 678 through 699 Processing helix chain 'B' and resid 700 through 703 removed outlier: 4.049A pdb=" N SER B 703 " --> pdb=" O ASN B 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 700 through 703' Processing helix chain 'B' and resid 712 through 731 Processing helix chain 'B' and resid 735 through 749 Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 15 through 25 Processing helix chain 'C' and resid 26 through 34 removed outlier: 4.313A pdb=" N ASN C 31 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 54 removed outlier: 3.791A pdb=" N CYS C 54 " --> pdb=" O LYS C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 70 removed outlier: 3.895A pdb=" N ILE C 70 " --> pdb=" O MET C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 105 removed outlier: 3.553A pdb=" N VAL C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 117 Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 157 through 170 Processing helix chain 'C' and resid 171 through 175 removed outlier: 3.887A pdb=" N ALA C 174 " --> pdb=" O PRO C 171 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY C 175 " --> pdb=" O LYS C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 171 through 175' Processing helix chain 'C' and resid 178 through 184 removed outlier: 3.547A pdb=" N TRP C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 195 Processing helix chain 'C' and resid 201 through 214 Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 233 through 238 removed outlier: 3.653A pdb=" N GLN C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 274 removed outlier: 4.543A pdb=" N VAL C 274 " --> pdb=" O ARG C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 287 removed outlier: 3.547A pdb=" N LEU C 281 " --> pdb=" O ASN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 303 Processing helix chain 'C' and resid 307 through 318 Processing helix chain 'C' and resid 392 through 408 Processing helix chain 'C' and resid 409 through 415 Processing helix chain 'C' and resid 431 through 443 removed outlier: 3.687A pdb=" N ASN C 442 " --> pdb=" O ARG C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.883A pdb=" N GLY C 452 " --> pdb=" O PHE C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 537 through 541 removed outlier: 3.672A pdb=" N MET C 540 " --> pdb=" O MET C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 557 Processing helix chain 'C' and resid 557 through 568 Processing helix chain 'C' and resid 570 through 574 removed outlier: 3.721A pdb=" N PHE C 573 " --> pdb=" O GLU C 570 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN C 574 " --> pdb=" O ASP C 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 570 through 574' Processing helix chain 'C' and resid 575 through 583 removed outlier: 3.668A pdb=" N SER C 583 " --> pdb=" O GLU C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 607 removed outlier: 4.251A pdb=" N GLY C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLN C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 619 Processing helix chain 'C' and resid 682 through 688 removed outlier: 4.162A pdb=" N ARG C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASN C 687 " --> pdb=" O ASP C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 694 removed outlier: 3.989A pdb=" N ASN C 692 " --> pdb=" O SER C 689 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL C 694 " --> pdb=" O GLY C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 719 removed outlier: 3.571A pdb=" N LYS C 719 " --> pdb=" O GLU C 715 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79 Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 256 Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 294 removed outlier: 4.178A pdb=" N TYR A 476 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.514A pdb=" N VAL A 538 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL A 553 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SER A 543 " --> pdb=" O LYS A 551 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS A 551 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TYR A 497 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER A 492 " --> pdb=" O ASN A 487 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASN A 487 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ASP A 494 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL A 485 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU A 496 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASN A 483 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY A 498 " --> pdb=" O ILE A 481 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 373 through 374 removed outlier: 5.942A pdb=" N GLN A 373 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N GLN B 367 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 623 through 628 removed outlier: 3.504A pdb=" N GLY A 618 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLY A 627 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N SER A 616 " --> pdb=" O GLY A 627 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 190 Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.603A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 488 through 491 Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AB4, first strand: chain 'C' and resid 73 through 74 Processing sheet with id=AB5, first strand: chain 'C' and resid 131 through 137 removed outlier: 5.663A pdb=" N ILE C 245 " --> pdb=" O GLY C 133 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE C 135 " --> pdb=" O ARG C 243 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG C 243 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 143 through 148 Processing sheet with id=AB7, first strand: chain 'C' and resid 294 through 295 Processing sheet with id=AB8, first strand: chain 'C' and resid 324 through 326 removed outlier: 5.214A pdb=" N LEU C 332 " --> pdb=" O ARG C 368 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ARG C 368 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ARG C 334 " --> pdb=" O HIS C 366 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N HIS C 366 " --> pdb=" O ARG C 334 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ARG C 373 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER C 379 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 342 through 347 Processing sheet with id=AC1, first strand: chain 'C' and resid 453 through 455 Processing sheet with id=AC2, first strand: chain 'C' and resid 498 through 499 Processing sheet with id=AC3, first strand: chain 'C' and resid 639 through 641 Processing sheet with id=AC4, first strand: chain 'C' and resid 660 through 662 Processing sheet with id=AC5, first strand: chain 'C' and resid 699 through 702 removed outlier: 7.119A pdb=" N LYS C 737 " --> pdb=" O SER C 701 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LYS C 734 " --> pdb=" O LEU C 730 " (cutoff:3.500A) 892 hydrogen bonds defined for protein. 2466 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 8.47 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 17659 1.04 - 1.24: 2405 1.24 - 1.44: 5458 1.44 - 1.65: 10378 1.65 - 1.85: 226 Bond restraints: 36126 Sorted by residual: bond pdb=" C5 GTA M 101 " pdb=" C6 GTA M 101 " ideal model delta sigma weight residual 1.422 1.331 0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C2C GTA M 101 " pdb=" N3C GTA M 101 " ideal model delta sigma weight residual 1.322 1.397 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C5C GTA M 101 " pdb=" C6C GTA M 101 " ideal model delta sigma weight residual 1.404 1.331 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C1A GTA M 101 " pdb=" O4A GTA M 101 " ideal model delta sigma weight residual 1.390 1.454 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C2C GTA M 101 " pdb=" N1C GTA M 101 " ideal model delta sigma weight residual 1.331 1.394 -0.063 2.00e-02 2.50e+03 9.88e+00 ... (remaining 36121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 65067 2.07 - 4.14: 275 4.14 - 6.22: 19 6.22 - 8.29: 6 8.29 - 10.36: 4 Bond angle restraints: 65371 Sorted by residual: angle pdb=" N1C GTA M 101 " pdb=" C2C GTA M 101 " pdb=" N3C GTA M 101 " ideal model delta sigma weight residual 128.44 118.08 10.36 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C5 GTA M 101 " pdb=" C6 GTA M 101 " pdb=" N1 GTA M 101 " ideal model delta sigma weight residual 109.94 119.71 -9.77 3.00e+00 1.11e-01 1.06e+01 angle pdb=" O13 GTA M 101 " pdb=" P2 GTA M 101 " pdb=" O23 GTA M 101 " ideal model delta sigma weight residual 93.83 102.28 -8.45 3.00e+00 1.11e-01 7.94e+00 angle pdb=" C5 GTA M 101 " pdb=" C6 GTA M 101 " pdb=" O6 GTA M 101 " ideal model delta sigma weight residual 129.13 120.77 8.36 3.00e+00 1.11e-01 7.77e+00 angle pdb=" C2C GTA M 101 " pdb=" N3C GTA M 101 " pdb=" C4C GTA M 101 " ideal model delta sigma weight residual 111.78 119.83 -8.05 3.00e+00 1.11e-01 7.20e+00 ... (remaining 65366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 16516 35.40 - 70.80: 392 70.80 - 106.21: 25 106.21 - 141.61: 1 141.61 - 177.01: 5 Dihedral angle restraints: 16939 sinusoidal: 9734 harmonic: 7205 Sorted by residual: dihedral pdb=" C5A GTA M 101 " pdb=" O15 GTA M 101 " pdb=" P1 GTA M 101 " pdb=" O11 GTA M 101 " ideal model delta sinusoidal sigma weight residual -144.55 -32.42 -112.13 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" N3 G R 14 " pdb=" C2 G R 14 " pdb=" N2 G R 14 " pdb=" H22 G R 14 " ideal model delta sinusoidal sigma weight residual 0.00 -177.01 177.01 1 4.00e+01 6.25e-04 1.20e+01 dihedral pdb=" N3 G R 18 " pdb=" C2 G R 18 " pdb=" N2 G R 18 " pdb=" H22 G R 18 " ideal model delta sinusoidal sigma weight residual 0.00 176.35 -176.35 1 4.00e+01 6.25e-04 1.20e+01 ... (remaining 16936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2526 0.063 - 0.125: 238 0.125 - 0.188: 15 0.188 - 0.251: 0 0.251 - 0.314: 2 Chirality restraints: 2781 Sorted by residual: chirality pdb=" C4B GTA M 101 " pdb=" C3B GTA M 101 " pdb=" C5B GTA M 101 " pdb=" O4B GTA M 101 " both_signs ideal model delta sigma weight residual False -2.53 -2.85 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C4A GTA M 101 " pdb=" C3A GTA M 101 " pdb=" C5A GTA M 101 " pdb=" O4A GTA M 101 " both_signs ideal model delta sigma weight residual False -2.54 -2.81 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C2A GTA M 101 " pdb=" C1A GTA M 101 " pdb=" C3A GTA M 101 " pdb=" O2A GTA M 101 " both_signs ideal model delta sigma weight residual False -2.54 -2.70 0.16 2.00e-01 2.50e+01 6.75e-01 ... (remaining 2778 not shown) Planarity restraints: 5144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " -0.022 2.00e-02 2.50e+03 8.71e-03 2.47e+00 pdb=" N9 A V 4 " 0.021 2.00e-02 2.50e+03 pdb=" C8 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A V 4 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A V 4 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A V 4 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A V 4 " 0.005 2.00e-02 2.50e+03 pdb=" H8 A V 4 " 0.002 2.00e-02 2.50e+03 pdb=" H2 A V 4 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A V 7 " -0.019 2.00e-02 2.50e+03 7.65e-03 1.90e+00 pdb=" N9 A V 7 " 0.019 2.00e-02 2.50e+03 pdb=" C8 A V 7 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A V 7 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 7 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A V 7 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A V 7 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A V 7 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A V 7 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A V 7 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A V 7 " 0.003 2.00e-02 2.50e+03 pdb=" H8 A V 7 " 0.001 2.00e-02 2.50e+03 pdb=" H2 A V 7 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A R 17 " 0.018 2.00e-02 2.50e+03 7.28e-03 1.72e+00 pdb=" N9 A R 17 " -0.017 2.00e-02 2.50e+03 pdb=" C8 A R 17 " -0.005 2.00e-02 2.50e+03 pdb=" N7 A R 17 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A R 17 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A R 17 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A R 17 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A R 17 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A R 17 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A R 17 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A R 17 " -0.002 2.00e-02 2.50e+03 pdb=" H8 A R 17 " -0.000 2.00e-02 2.50e+03 pdb=" H2 A R 17 " -0.002 2.00e-02 2.50e+03 ... (remaining 5141 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1302 2.16 - 2.77: 71252 2.77 - 3.38: 106406 3.38 - 3.99: 139405 3.99 - 4.60: 219707 Nonbonded interactions: 538072 Sorted by model distance: nonbonded pdb=" O GLY C 357 " pdb="HE22 GLN C 408 " model vdw 1.546 2.450 nonbonded pdb=" H GLY B 157 " pdb=" OD2 ASP B 169 " model vdw 1.558 2.450 nonbonded pdb=" OE1 GLU A 333 " pdb=" H GLU A 333 " model vdw 1.588 2.450 nonbonded pdb=" OE2 GLU C 155 " pdb="HH12 ARG C 217 " model vdw 1.590 2.450 nonbonded pdb=" O ALA C 580 " pdb=" HG SER C 583 " model vdw 1.592 2.450 ... (remaining 538067 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.220 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: 0.240 Extract box with map and model: 0.590 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 37.610 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 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 : 0.007 0.804 18429 Z= 0.609 Angle : 0.479 10.361 25015 Z= 0.241 Chirality : 0.038 0.314 2781 Planarity : 0.003 0.037 3058 Dihedral : 12.694 112.132 7308 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.25 % Favored : 97.71 % Rotamer: Outliers : 1.12 % Allowed : 4.25 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.19), residues: 2138 helix: 2.05 (0.17), residues: 979 sheet: -0.94 (0.33), residues: 243 loop : -0.25 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 211 TYR 0.014 0.001 TYR B 554 PHE 0.010 0.001 PHE B 550 TRP 0.014 0.001 TRP B 437 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00289 (18427) covalent geometry : angle 0.47857 (25015) hydrogen bonds : bond 0.13406 ( 918) hydrogen bonds : angle 5.44355 ( 2518) Misc. bond : bond 0.56922 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 321 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 300 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 655 ASP cc_start: 0.7739 (p0) cc_final: 0.7362 (p0) REVERT: C 66 MET cc_start: 0.8689 (mmt) cc_final: 0.8377 (mmt) REVERT: C 92 MET cc_start: 0.8071 (mmt) cc_final: 0.7870 (mmt) outliers start: 21 outliers final: 4 residues processed: 318 average time/residue: 1.5308 time to fit residues: 537.2813 Evaluate side-chains 196 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 192 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain C residue 332 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN C 37 ASN C 470 ASN C 592 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.071556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.055991 restraints weight = 134788.163| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.04 r_work: 0.2812 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18429 Z= 0.243 Angle : 0.569 6.936 25015 Z= 0.295 Chirality : 0.040 0.154 2781 Planarity : 0.004 0.049 3058 Dihedral : 11.289 106.296 2966 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.23 % Favored : 96.73 % Rotamer: Outliers : 1.17 % Allowed : 11.00 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.18), residues: 2138 helix: 1.86 (0.16), residues: 988 sheet: -0.72 (0.34), residues: 225 loop : -0.37 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 562 TYR 0.014 0.001 TYR A 644 PHE 0.017 0.001 PHE A 118 TRP 0.012 0.001 TRP B 437 HIS 0.006 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00531 (18427) covalent geometry : angle 0.56854 (25015) hydrogen bonds : bond 0.04560 ( 918) hydrogen bonds : angle 4.84823 ( 2518) Misc. bond : bond 0.00386 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 655 ASP cc_start: 0.8447 (p0) cc_final: 0.8140 (p0) outliers start: 22 outliers final: 12 residues processed: 210 average time/residue: 1.4601 time to fit residues: 341.9456 Evaluate side-chains 191 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 693 ASN Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 388 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 143 optimal weight: 2.9990 chunk 196 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 470 ASN C 592 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.071551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.055887 restraints weight = 134882.093| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.06 r_work: 0.2814 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18429 Z= 0.180 Angle : 0.522 5.607 25015 Z= 0.270 Chirality : 0.039 0.158 2781 Planarity : 0.004 0.035 3058 Dihedral : 10.967 98.749 2963 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.90 % Favored : 97.05 % Rotamer: Outliers : 1.01 % Allowed : 11.32 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.18), residues: 2138 helix: 1.87 (0.16), residues: 989 sheet: -0.95 (0.33), residues: 231 loop : -0.37 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 417 TYR 0.013 0.001 TYR B 554 PHE 0.011 0.001 PHE B 550 TRP 0.012 0.001 TRP B 437 HIS 0.005 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00394 (18427) covalent geometry : angle 0.52169 (25015) hydrogen bonds : bond 0.04122 ( 918) hydrogen bonds : angle 4.71029 ( 2518) Misc. bond : bond 0.00045 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 GLU cc_start: 0.8452 (tt0) cc_final: 0.8223 (tt0) REVERT: B 655 ASP cc_start: 0.8395 (p0) cc_final: 0.8065 (p0) outliers start: 19 outliers final: 11 residues processed: 203 average time/residue: 1.4018 time to fit residues: 319.2690 Evaluate side-chains 188 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 388 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 150 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 470 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.069080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.053660 restraints weight = 136313.090| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.03 r_work: 0.2758 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 18429 Z= 0.301 Angle : 0.575 7.738 25015 Z= 0.300 Chirality : 0.041 0.157 2781 Planarity : 0.004 0.037 3058 Dihedral : 10.836 94.793 2963 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.74 % Favored : 96.21 % Rotamer: Outliers : 1.33 % Allowed : 11.11 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.18), residues: 2138 helix: 1.70 (0.16), residues: 984 sheet: -0.91 (0.34), residues: 225 loop : -0.49 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 417 TYR 0.016 0.002 TYR C 117 PHE 0.016 0.002 PHE B 495 TRP 0.012 0.002 TRP B 437 HIS 0.005 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00658 (18427) covalent geometry : angle 0.57520 (25015) hydrogen bonds : bond 0.04394 ( 918) hydrogen bonds : angle 4.78625 ( 2518) Misc. bond : bond 0.00124 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 204 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.8423 (mt) cc_final: 0.8183 (mt) REVERT: B 669 ARG cc_start: 0.5662 (mtm180) cc_final: 0.5450 (mtt90) outliers start: 25 outliers final: 12 residues processed: 196 average time/residue: 1.4041 time to fit residues: 308.9821 Evaluate side-chains 181 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 675 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 132 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 192 optimal weight: 0.5980 chunk 204 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 GLN C 37 ASN C 470 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.070856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.055425 restraints weight = 135189.753| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.06 r_work: 0.2800 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18429 Z= 0.137 Angle : 0.515 6.929 25015 Z= 0.264 Chirality : 0.038 0.157 2781 Planarity : 0.003 0.037 3058 Dihedral : 10.803 94.703 2963 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.13 % Favored : 96.82 % Rotamer: Outliers : 1.22 % Allowed : 11.74 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.18), residues: 2138 helix: 1.83 (0.16), residues: 1001 sheet: -0.99 (0.33), residues: 229 loop : -0.44 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 417 TYR 0.013 0.001 TYR B 554 PHE 0.012 0.001 PHE A 461 TRP 0.011 0.001 TRP B 437 HIS 0.006 0.001 HIS B 711 Details of bonding type rmsd covalent geometry : bond 0.00300 (18427) covalent geometry : angle 0.51452 (25015) hydrogen bonds : bond 0.03799 ( 918) hydrogen bonds : angle 4.61430 ( 2518) Misc. bond : bond 0.00033 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.7576 (t80) cc_final: 0.7299 (t80) REVERT: A 180 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7679 (mp0) outliers start: 23 outliers final: 10 residues processed: 191 average time/residue: 1.4833 time to fit residues: 317.0503 Evaluate side-chains 180 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 169 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 388 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 180 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 125 optimal weight: 0.2980 chunk 186 optimal weight: 0.5980 chunk 190 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN B 108 GLN C 37 ASN C 470 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.070511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.055138 restraints weight = 134978.973| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.05 r_work: 0.2799 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18429 Z= 0.156 Angle : 0.516 7.252 25015 Z= 0.263 Chirality : 0.038 0.155 2781 Planarity : 0.003 0.036 3058 Dihedral : 10.739 94.371 2963 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.46 % Favored : 96.49 % Rotamer: Outliers : 1.01 % Allowed : 12.06 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.18), residues: 2138 helix: 1.89 (0.16), residues: 1001 sheet: -0.92 (0.34), residues: 226 loop : -0.42 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 417 TYR 0.013 0.001 TYR A 644 PHE 0.012 0.001 PHE A 461 TRP 0.012 0.001 TRP B 437 HIS 0.004 0.001 HIS B 711 Details of bonding type rmsd covalent geometry : bond 0.00345 (18427) covalent geometry : angle 0.51574 (25015) hydrogen bonds : bond 0.03764 ( 918) hydrogen bonds : angle 4.55762 ( 2518) Misc. bond : bond 0.00030 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: A 180 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: B 108 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8149 (tm130) outliers start: 19 outliers final: 10 residues processed: 190 average time/residue: 1.3340 time to fit residues: 284.2600 Evaluate side-chains 184 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 675 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 104 optimal weight: 0.3980 chunk 183 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 470 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.070551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.055171 restraints weight = 135505.786| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.06 r_work: 0.2799 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18429 Z= 0.158 Angle : 0.517 7.558 25015 Z= 0.265 Chirality : 0.038 0.155 2781 Planarity : 0.003 0.036 3058 Dihedral : 10.726 94.596 2963 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.51 % Favored : 96.45 % Rotamer: Outliers : 0.90 % Allowed : 12.43 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.18), residues: 2138 helix: 1.88 (0.16), residues: 1001 sheet: -0.91 (0.34), residues: 226 loop : -0.42 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 417 TYR 0.013 0.001 TYR A 644 PHE 0.011 0.001 PHE A 461 TRP 0.012 0.001 TRP B 437 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00347 (18427) covalent geometry : angle 0.51740 (25015) hydrogen bonds : bond 0.03750 ( 918) hydrogen bonds : angle 4.53901 ( 2518) Misc. bond : bond 0.00022 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: A 180 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: B 724 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8317 (m-30) outliers start: 17 outliers final: 11 residues processed: 191 average time/residue: 1.3664 time to fit residues: 293.2736 Evaluate side-chains 186 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 724 ASP Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 675 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 196 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 201 optimal weight: 0.5980 chunk 198 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 204 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN B 108 GLN C 37 ASN C 470 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.070764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.055638 restraints weight = 135184.756| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.05 r_work: 0.2810 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18429 Z= 0.124 Angle : 0.510 8.142 25015 Z= 0.258 Chirality : 0.038 0.201 2781 Planarity : 0.003 0.036 3058 Dihedral : 10.687 94.063 2963 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.37 % Favored : 96.59 % Rotamer: Outliers : 0.80 % Allowed : 12.96 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.18), residues: 2138 helix: 1.98 (0.16), residues: 1001 sheet: -0.92 (0.34), residues: 228 loop : -0.36 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 417 TYR 0.013 0.001 TYR B 729 PHE 0.010 0.001 PHE A 461 TRP 0.011 0.001 TRP B 437 HIS 0.004 0.001 HIS B 711 Details of bonding type rmsd covalent geometry : bond 0.00276 (18427) covalent geometry : angle 0.50980 (25015) hydrogen bonds : bond 0.03560 ( 918) hydrogen bonds : angle 4.45486 ( 2518) Misc. bond : bond 0.00016 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: A 642 MET cc_start: 0.9106 (mmp) cc_final: 0.8413 (mmp) REVERT: B 108 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8284 (tm-30) REVERT: B 655 ASP cc_start: 0.8163 (p0) cc_final: 0.7913 (p0) REVERT: B 724 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8312 (m-30) outliers start: 15 outliers final: 10 residues processed: 188 average time/residue: 1.4840 time to fit residues: 312.1648 Evaluate side-chains 185 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 669 ARG Chi-restraints excluded: chain B residue 724 ASP Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 675 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 193 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 205 optimal weight: 0.1980 chunk 40 optimal weight: 0.0980 chunk 96 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN C 470 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.070943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.055914 restraints weight = 135088.315| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.04 r_work: 0.2820 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18429 Z= 0.120 Angle : 0.517 8.310 25015 Z= 0.261 Chirality : 0.037 0.183 2781 Planarity : 0.003 0.036 3058 Dihedral : 10.651 93.717 2963 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.27 % Favored : 96.68 % Rotamer: Outliers : 0.69 % Allowed : 13.39 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.18), residues: 2138 helix: 2.01 (0.16), residues: 1001 sheet: -0.87 (0.34), residues: 229 loop : -0.35 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 443 TYR 0.016 0.001 TYR C 439 PHE 0.010 0.001 PHE A 461 TRP 0.011 0.001 TRP B 437 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00270 (18427) covalent geometry : angle 0.51726 (25015) hydrogen bonds : bond 0.03555 ( 918) hydrogen bonds : angle 4.42737 ( 2518) Misc. bond : bond 0.00010 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: A 642 MET cc_start: 0.9112 (mmp) cc_final: 0.8648 (mmp) REVERT: B 655 ASP cc_start: 0.8157 (p0) cc_final: 0.7902 (p0) REVERT: C 443 ARG cc_start: 0.8363 (mtp180) cc_final: 0.7830 (mmm-85) outliers start: 13 outliers final: 11 residues processed: 185 average time/residue: 1.4938 time to fit residues: 309.1454 Evaluate side-chains 183 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 675 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 204 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 0.0060 chunk 122 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 82 optimal weight: 0.0770 chunk 194 optimal weight: 0.8980 chunk 188 optimal weight: 0.9980 overall best weight: 0.4954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 470 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.071344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.056339 restraints weight = 135223.143| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.05 r_work: 0.2832 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18429 Z= 0.111 Angle : 0.516 9.430 25015 Z= 0.259 Chirality : 0.037 0.185 2781 Planarity : 0.003 0.036 3058 Dihedral : 10.597 92.905 2963 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.27 % Favored : 96.68 % Rotamer: Outliers : 0.69 % Allowed : 13.39 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.19), residues: 2138 helix: 2.06 (0.16), residues: 1002 sheet: -0.79 (0.34), residues: 229 loop : -0.32 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 417 TYR 0.013 0.001 TYR B 554 PHE 0.009 0.001 PHE A 461 TRP 0.018 0.001 TRP C 182 HIS 0.004 0.001 HIS B 711 Details of bonding type rmsd covalent geometry : bond 0.00252 (18427) covalent geometry : angle 0.51573 (25015) hydrogen bonds : bond 0.03444 ( 918) hydrogen bonds : angle 4.36618 ( 2518) Misc. bond : bond 0.00010 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: A 185 ASN cc_start: 0.8958 (t0) cc_final: 0.8513 (t0) REVERT: A 642 MET cc_start: 0.9118 (mmp) cc_final: 0.8635 (mmp) REVERT: A 705 GLU cc_start: 0.8309 (tt0) cc_final: 0.8091 (tt0) REVERT: B 655 ASP cc_start: 0.8150 (p0) cc_final: 0.7910 (p0) REVERT: C 450 GLN cc_start: 0.6517 (mp10) cc_final: 0.6312 (mp10) outliers start: 13 outliers final: 10 residues processed: 185 average time/residue: 1.4991 time to fit residues: 311.2653 Evaluate side-chains 181 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 470 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.0470 chunk 40 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.071372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.056369 restraints weight = 134882.672| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.04 r_work: 0.2830 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.243 18429 Z= 0.208 Angle : 0.697 59.165 25015 Z= 0.398 Chirality : 0.038 0.269 2781 Planarity : 0.003 0.036 3058 Dihedral : 10.599 92.907 2963 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.32 % Favored : 96.63 % Rotamer: Outliers : 0.58 % Allowed : 13.50 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.19), residues: 2138 helix: 2.07 (0.16), residues: 1002 sheet: -0.79 (0.34), residues: 229 loop : -0.32 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 417 TYR 0.013 0.001 TYR B 554 PHE 0.013 0.001 PHE A 118 TRP 0.015 0.001 TRP C 182 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00388 (18427) covalent geometry : angle 0.69716 (25015) hydrogen bonds : bond 0.03445 ( 918) hydrogen bonds : angle 4.36704 ( 2518) Misc. bond : bond 0.00012 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10366.37 seconds wall clock time: 176 minutes 16.67 seconds (10576.67 seconds total)