Starting phenix.real_space_refine on Thu Sep 18 16:47:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qct_4512/09_2025/6qct_4512.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qct_4512/09_2025/6qct_4512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qct_4512/09_2025/6qct_4512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qct_4512/09_2025/6qct_4512.map" model { file = "/net/cci-nas-00/data/ceres_data/6qct_4512/09_2025/6qct_4512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qct_4512/09_2025/6qct_4512.cif" } resolution = 3.2 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= 0.003 sd= 0.026 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: 6 Type Number sf(0) Gaussians P 41 5.49 5 Mg 2 5.21 5 S 132 5.16 5 C 11414 2.51 5 N 3150 2.21 5 O 3527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18266 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 722, 5793 Classifications: {'peptide': 722} Link IDs: {'PTRANS': 26, 'TRANS': 695} Chain: "B" Number of atoms: 5774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5774 Classifications: {'peptide': 735} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 700} Chain breaks: 1 Chain: "C" Number of atoms: 5832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5832 Classifications: {'peptide': 729} Incomplete info: {'truncation_to_alanine': 1} 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: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 284 Classifications: {'RNA': 13} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna2p': 4, 'rna3p': 8} Chain: "R" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 268 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 8} Link IDs: {'rna2p': 2, 'rna3p': 10} Chain: "M" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 313 Unusual residues: {'GTG': 1} Classifications: {'RNA': 12, 'undetermined': 1} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 10, None: 1} Not linked: pdbres="GTG M 1 " pdbres=" A M 2 " 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.57, per 1000 atoms: 0.25 Number of scatterers: 18266 At special positions: 0 Unit cell: (122.172, 127.989, 120.509, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 132 16.00 P 41 15.00 Mg 2 11.99 O 3527 8.00 N 3150 7.00 C 11414 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 772.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4070 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 22 sheets defined 48.5% alpha, 12.7% beta 10 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 Processing helix chain 'A' and resid 10 through 23 Processing helix chain 'A' and resid 27 through 30 removed outlier: 3.910A pdb=" N LEU A 30 " --> pdb=" O ASP A 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 27 through 30' Processing helix chain 'A' and resid 31 through 49 removed outlier: 3.567A pdb=" N LEU A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER A 49 " --> pdb=" O CYS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.933A pdb=" N GLN A 71 " --> pdb=" O GLY A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 99 removed outlier: 3.554A pdb=" N HIS A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 139 removed outlier: 3.686A pdb=" N TYR A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU A 137 " --> pdb=" O TRP A 133 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 184 removed outlier: 3.839A pdb=" N LYS A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.530A pdb=" N GLY A 192 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 214 removed outlier: 3.652A pdb=" N ARG A 210 " --> pdb=" O GLN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.548A pdb=" N MET A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 266 through 271 removed outlier: 3.727A pdb=" N ILE A 269 " --> pdb=" O GLY A 266 " (cutoff:3.500A) 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 348 Processing helix chain 'A' and resid 359 through 367 Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 402 through 411 Processing helix chain 'A' and resid 429 through 447 removed outlier: 4.280A pdb=" N TYR A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 472 removed outlier: 3.620A pdb=" N THR A 453 " --> pdb=" O CYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 573 through 576 Processing helix chain 'A' and resid 577 through 596 removed outlier: 4.055A pdb=" N GLN A 583 " --> pdb=" O GLN A 579 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 596 " --> pdb=" O SER A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 605 Processing helix chain 'A' and resid 628 through 646 Processing helix chain 'A' and resid 648 through 670 removed outlier: 3.990A pdb=" N LEU A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A 664 " --> pdb=" O ARG A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 687 removed outlier: 3.813A pdb=" N ILE A 686 " --> pdb=" O MET A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 714 Processing helix chain 'A' and resid 715 through 720 removed outlier: 4.982A pdb=" N GLU A 718 " --> pdb=" O LYS A 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 12 removed outlier: 4.080A pdb=" N ASP B 11 " --> pdb=" O PHE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.876A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.700A pdb=" N THR B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 99 removed outlier: 3.604A pdb=" N HIS B 99 " --> pdb=" O MET B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 115 Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.606A pdb=" N LYS B 121 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 151 Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.732A pdb=" N LYS B 160 " --> pdb=" O GLY B 157 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY B 161 " --> pdb=" O ALA B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 174 removed outlier: 3.510A 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 264 removed outlier: 3.669A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 292 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.791A pdb=" N ALA B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 326 " --> pdb=" O THR B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 344 removed outlier: 4.481A 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 372 through 376 removed outlier: 4.228A pdb=" N ILE B 376 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.645A pdb=" N TYR B 381 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 removed outlier: 3.598A pdb=" N LYS B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 426 Processing helix chain 'B' and resid 454 through 471 removed outlier: 3.515A pdb=" N LEU B 471 " --> pdb=" O ARG B 467 " (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 571 through 582 Processing helix chain 'B' and resid 584 through 588 Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 599 through 603 removed outlier: 3.805A pdb=" N ASN B 602 " --> pdb=" O ASN B 599 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 599 through 603' Processing helix chain 'B' and resid 606 through 611 Processing helix chain 'B' and resid 616 through 624 Processing helix chain 'B' and resid 679 through 699 removed outlier: 3.751A pdb=" N GLU B 685 " --> pdb=" O MET B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 704 removed outlier: 4.286A pdb=" N SER B 703 " --> pdb=" O ASN B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 731 Processing helix chain 'B' and resid 735 through 747 Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 15 through 25 removed outlier: 3.690A pdb=" N THR C 20 " --> pdb=" O ASN C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 28 No H-bonds generated for 'chain 'C' and resid 26 through 28' Processing helix chain 'C' and resid 29 through 35 removed outlier: 4.308A pdb=" N LYS C 35 " --> pdb=" O ASN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 53 Processing helix chain 'C' and resid 66 through 70 removed outlier: 3.622A pdb=" N ARG C 69 " --> pdb=" O MET C 66 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 70 " --> pdb=" O ALA C 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 66 through 70' Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.532A pdb=" N ASP C 85 " --> pdb=" O ASN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 105 removed outlier: 3.839A pdb=" N VAL C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 117 through 129 removed outlier: 3.594A pdb=" N LEU C 127 " --> pdb=" O ARG C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 170 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 removed outlier: 3.655A pdb=" N GLU C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 removed outlier: 3.738A pdb=" N GLN C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 273 Processing helix chain 'C' and resid 277 through 288 removed outlier: 3.795A pdb=" N LEU C 281 " --> pdb=" O ASN C 277 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS C 288 " --> pdb=" O GLU C 284 " (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 removed outlier: 3.737A pdb=" N GLN C 408 " --> pdb=" O MET C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 415 removed outlier: 3.515A pdb=" N PHE C 413 " --> pdb=" O ASP C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 440 Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.775A pdb=" N GLY C 452 " --> pdb=" O PHE C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 541 removed outlier: 4.066A pdb=" N GLU C 539 " --> pdb=" O LYS C 536 " (cutoff:3.500A) removed outlier: 3.898A 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 575 through 583 removed outlier: 3.638A pdb=" N ALA C 580 " --> pdb=" O ASP C 576 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER C 583 " --> pdb=" O GLU C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 607 removed outlier: 4.569A pdb=" N GLY C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 4.610A 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 689 through 694 removed outlier: 3.834A pdb=" N ASN C 692 " --> pdb=" O SER C 689 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL C 694 " --> pdb=" O GLY C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 719 removed outlier: 3.703A pdb=" N LYS C 719 " --> pdb=" O GLU C 715 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.543A pdb=" N PHE A 118 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N MET A 146 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU A 120 " --> pdb=" O MET A 146 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N PHE A 148 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY A 122 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 255 through 256 Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 293 removed outlier: 5.147A pdb=" N ASP A 494 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 485 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LEU A 496 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN A 483 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY A 498 " --> pdb=" O ILE A 481 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR A 476 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 291 through 293 removed outlier: 7.215A pdb=" N TYR A 497 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 542 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU A 555 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ARG A 540 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N CYS A 557 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL A 538 " --> pdb=" O CYS A 557 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 373 through 374 removed outlier: 5.947A pdb=" N GLN A 373 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLN B 367 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 623 through 627 removed outlier: 6.583A pdb=" N LYS A 623 " --> pdb=" O THR A 619 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR A 619 " --> pdb=" O LYS A 623 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A 625 " --> pdb=" O ILE A 617 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 192 Processing sheet with id=AB2, first strand: chain 'B' and resid 240 through 243 removed outlier: 3.868A pdb=" N THR B 226 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 306 through 307 removed outlier: 4.517A pdb=" N ASN B 475 " --> pdb=" O THR B 307 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 488 through 491 Processing sheet with id=AB5, first strand: chain 'C' and resid 131 through 137 removed outlier: 5.352A pdb=" N TRP C 132 " --> pdb=" O HIS C 247 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N HIS C 247 " --> pdb=" O TRP C 132 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG C 134 " --> pdb=" O ILE C 245 " (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 removed outlier: 3.874A pdb=" N GLU C 294 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 324 through 327 removed outlier: 3.716A pdb=" N LEU C 330 " --> pdb=" O PHE C 327 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLU C 364 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY C 337 " --> pdb=" O GLU C 362 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLU C 362 " --> pdb=" O GLY C 337 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER C 379 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL C 480 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU C 386 " --> pdb=" O VAL C 480 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR C 482 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ILE C 388 " --> pdb=" O THR C 482 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS C 463 " --> pdb=" O VAL C 481 " (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 454 Processing sheet with id=AC2, first strand: chain 'C' and resid 639 through 641 Processing sheet with id=AC3, first strand: chain 'C' and resid 660 through 662 Processing sheet with id=AC4, first strand: chain 'C' and resid 725 through 729 798 hydrogen bonds defined for protein. 2253 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 3.59 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4961 1.33 - 1.45: 3317 1.45 - 1.57: 10112 1.57 - 1.69: 78 1.69 - 1.81: 224 Bond restraints: 18692 Sorted by residual: bond pdb=" C5B GTG M 1 " pdb=" C6B GTG M 1 " ideal model delta sigma weight residual 1.424 1.321 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C5A GTG M 1 " pdb=" C6A GTG M 1 " ideal model delta sigma weight residual 1.427 1.339 0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C1E GTG M 1 " pdb=" O4E GTG M 1 " ideal model delta sigma weight residual 1.392 1.466 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" O3A GTG M 1 " pdb=" PB GTG M 1 " ideal model delta sigma weight residual 1.656 1.601 0.055 2.00e-02 2.50e+03 7.68e+00 bond pdb=" O5D GTG M 1 " pdb=" PA GTG M 1 " ideal model delta sigma weight residual 1.653 1.599 0.054 2.00e-02 2.50e+03 7.29e+00 ... (remaining 18687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 24799 2.07 - 4.14: 480 4.14 - 6.22: 63 6.22 - 8.29: 22 8.29 - 10.36: 6 Bond angle restraints: 25370 Sorted by residual: angle pdb=" C LEU B 163 " pdb=" N ILE B 164 " pdb=" CA ILE B 164 " ideal model delta sigma weight residual 120.24 123.92 -3.68 6.30e-01 2.52e+00 3.41e+01 angle pdb=" C ILE C 291 " pdb=" N ASP C 292 " pdb=" CA ASP C 292 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 angle pdb=" C2' A V 4 " pdb=" C1' A V 4 " pdb=" N9 A V 4 " ideal model delta sigma weight residual 112.00 118.12 -6.12 1.50e+00 4.44e-01 1.66e+01 angle pdb=" CA TRP B 437 " pdb=" CB TRP B 437 " pdb=" CG TRP B 437 " ideal model delta sigma weight residual 113.60 120.75 -7.15 1.90e+00 2.77e-01 1.42e+01 angle pdb=" C ILE B 427 " pdb=" N LYS B 428 " pdb=" CA LYS B 428 " ideal model delta sigma weight residual 121.54 128.15 -6.61 1.91e+00 2.74e-01 1.20e+01 ... (remaining 25365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.00: 10299 19.00 - 38.00: 868 38.00 - 57.01: 230 57.01 - 76.01: 64 76.01 - 95.01: 15 Dihedral angle restraints: 11476 sinusoidal: 5159 harmonic: 6317 Sorted by residual: dihedral pdb=" CA GLN B 441 " pdb=" C GLN B 441 " pdb=" N SER B 442 " pdb=" CA SER B 442 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA GLU A 29 " pdb=" C GLU A 29 " pdb=" N LEU A 30 " pdb=" CA LEU A 30 " ideal model delta harmonic sigma weight residual 180.00 158.15 21.85 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA GLN C 607 " pdb=" C GLN C 607 " pdb=" N GLU C 608 " pdb=" CA GLU C 608 " ideal model delta harmonic sigma weight residual 180.00 -159.17 -20.83 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 11473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2080 0.050 - 0.100: 597 0.100 - 0.150: 122 0.150 - 0.200: 14 0.200 - 0.249: 3 Chirality restraints: 2816 Sorted by residual: chirality pdb=" C1' A V 4 " pdb=" O4' A V 4 " pdb=" C2' A V 4 " pdb=" N9 A V 4 " both_signs ideal model delta sigma weight residual False 2.46 2.21 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C4D GTG M 1 " pdb=" C3D GTG M 1 " pdb=" C5D GTG M 1 " pdb=" O4D GTG M 1 " both_signs ideal model delta sigma weight residual False -2.52 -2.74 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C1E GTG M 1 " pdb=" C2E GTG M 1 " pdb=" N9B GTG M 1 " pdb=" O4E GTG M 1 " both_signs ideal model delta sigma weight residual False 2.37 2.58 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 2813 not shown) Planarity restraints: 3112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " -0.041 2.00e-02 2.50e+03 1.96e-02 1.06e+01 pdb=" N9 A V 4 " 0.048 2.00e-02 2.50e+03 pdb=" C8 A V 4 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A V 4 " -0.004 2.00e-02 2.50e+03 pdb=" C5 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A V 4 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A V 4 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A V 4 " -0.005 2.00e-02 2.50e+03 pdb=" C2 A V 4 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A V 4 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A V 4 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 656 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO C 657 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 657 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 657 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 393 " -0.040 5.00e-02 4.00e+02 5.90e-02 5.57e+00 pdb=" N PRO B 394 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 394 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 394 " -0.034 5.00e-02 4.00e+02 ... (remaining 3109 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 245 2.64 - 3.20: 14745 3.20 - 3.77: 28073 3.77 - 4.33: 40189 4.33 - 4.90: 66172 Nonbonded interactions: 149424 Sorted by model distance: nonbonded pdb=" OD1 ASP B 445 " pdb="MG MG B 801 " model vdw 2.075 2.170 nonbonded pdb=" OD1 ASP A 109 " pdb="MG MG A 801 " model vdw 2.109 2.170 nonbonded pdb=" OE2 GLU A 81 " pdb="MG MG A 801 " model vdw 2.141 2.170 nonbonded pdb=" OD2 ASP B 445 " pdb="MG MG B 801 " model vdw 2.154 2.170 nonbonded pdb=" OD2 ASP B 521 " pdb=" OH TYR B 558 " model vdw 2.261 3.040 ... (remaining 149419 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: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.500 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 18693 Z= 0.281 Angle : 0.765 10.362 25370 Z= 0.411 Chirality : 0.048 0.249 2816 Planarity : 0.007 0.064 3112 Dihedral : 15.755 95.009 7406 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.87 % Allowed : 8.07 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.92 (0.13), residues: 2176 helix: -2.48 (0.12), residues: 948 sheet: -2.07 (0.31), residues: 231 loop : -2.78 (0.15), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 634 TYR 0.019 0.002 TYR C 207 PHE 0.016 0.002 PHE B 199 TRP 0.032 0.002 TRP B 437 HIS 0.007 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00643 (18692) covalent geometry : angle 0.76461 (25370) hydrogen bonds : bond 0.15211 ( 819) hydrogen bonds : angle 6.60551 ( 2303) Misc. bond : bond 0.04100 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 250 time to evaluate : 0.798 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: A 3 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8503 (t) REVERT: A 85 ARG cc_start: 0.7096 (mtt180) cc_final: 0.6803 (ttm-80) REVERT: A 165 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7200 (tp30) REVERT: C 208 MET cc_start: 0.7860 (ptm) cc_final: 0.7640 (ptt) REVERT: C 233 MET cc_start: 0.8845 (tpp) cc_final: 0.8449 (tpp) REVERT: C 584 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8446 (pp) outliers start: 112 outliers final: 35 residues processed: 345 average time/residue: 0.1819 time to fit residues: 90.1840 Evaluate side-chains 184 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 736 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 92 GLN A 222 ASN A 357 GLN A 462 HIS A 610 ASN A 693 ASN B 47 HIS B 265 ASN B 310 ASN B 314 ASN B 346 ASN B 475 ASN B 531 ASN ** B 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 627 GLN B 675 ASN B 680 ASN B 710 GLN C 323 GLN C 354 GLN ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN C 442 ASN C 552 GLN C 574 GLN C 614 GLN ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 727 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.067047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.053914 restraints weight = 52551.373| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.47 r_work: 0.2841 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18693 Z= 0.136 Angle : 0.543 6.799 25370 Z= 0.287 Chirality : 0.040 0.236 2816 Planarity : 0.005 0.042 3112 Dihedral : 12.021 95.069 3044 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.83 % Allowed : 11.73 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: -2.04 (0.16), residues: 2176 helix: -0.43 (0.16), residues: 976 sheet: -1.66 (0.32), residues: 231 loop : -2.22 (0.17), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 178 TYR 0.014 0.001 TYR A 154 PHE 0.011 0.001 PHE A 646 TRP 0.021 0.001 TRP B 437 HIS 0.003 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00302 (18692) covalent geometry : angle 0.54271 (25370) hydrogen bonds : bond 0.04132 ( 819) hydrogen bonds : angle 4.62560 ( 2303) Misc. bond : bond 0.00082 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 153 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 THR cc_start: 0.9153 (p) cc_final: 0.8751 (t) REVERT: A 50 ASP cc_start: 0.8506 (m-30) cc_final: 0.8290 (m-30) REVERT: A 165 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7959 (tp30) REVERT: C 208 MET cc_start: 0.8703 (ptm) cc_final: 0.8325 (ptt) REVERT: C 233 MET cc_start: 0.9072 (tpp) cc_final: 0.8629 (tpp) REVERT: C 237 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9145 (mm) REVERT: C 404 MET cc_start: 0.8221 (mtt) cc_final: 0.7886 (tpp) REVERT: C 537 MET cc_start: 0.8803 (tmm) cc_final: 0.8458 (tmm) REVERT: C 584 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8468 (pp) outliers start: 54 outliers final: 28 residues processed: 197 average time/residue: 0.1494 time to fit residues: 45.2524 Evaluate side-chains 166 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 527 GLN Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 736 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 84 optimal weight: 0.2980 chunk 51 optimal weight: 0.2980 chunk 115 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 162 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN B 314 ASN ** B 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 ASN ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 ASN C 502 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.067406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.054301 restraints weight = 52340.019| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.46 r_work: 0.2856 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18693 Z= 0.107 Angle : 0.487 8.427 25370 Z= 0.254 Chirality : 0.039 0.235 2816 Planarity : 0.004 0.042 3112 Dihedral : 11.433 92.701 3014 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.57 % Allowed : 12.15 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: -1.01 (0.17), residues: 2176 helix: 0.61 (0.17), residues: 971 sheet: -1.47 (0.31), residues: 251 loop : -1.79 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 85 TYR 0.014 0.001 TYR A 154 PHE 0.008 0.001 PHE A 223 TRP 0.016 0.001 TRP B 437 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00237 (18692) covalent geometry : angle 0.48734 (25370) hydrogen bonds : bond 0.03449 ( 819) hydrogen bonds : angle 4.20183 ( 2303) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 THR cc_start: 0.9143 (p) cc_final: 0.8745 (t) REVERT: A 97 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7845 (mp10) REVERT: A 154 TYR cc_start: 0.8391 (p90) cc_final: 0.8178 (p90) REVERT: A 544 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9087 (tp) REVERT: B 562 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7630 (ttp80) REVERT: B 685 GLU cc_start: 0.7623 (tt0) cc_final: 0.7292 (tm-30) REVERT: C 208 MET cc_start: 0.8595 (ptm) cc_final: 0.8246 (ptt) REVERT: C 233 MET cc_start: 0.8994 (tpp) cc_final: 0.8511 (tpp) REVERT: C 237 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9140 (mm) REVERT: C 537 MET cc_start: 0.8772 (tmm) cc_final: 0.8553 (tmm) outliers start: 49 outliers final: 24 residues processed: 187 average time/residue: 0.1529 time to fit residues: 43.8875 Evaluate side-chains 159 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 562 ARG Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 527 GLN Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 560 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 60 optimal weight: 6.9990 chunk 168 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 218 optimal weight: 8.9990 chunk 191 optimal weight: 9.9990 chunk 214 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 ASN C 366 HIS ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.063320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.050099 restraints weight = 53802.731| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.46 r_work: 0.2743 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 18693 Z= 0.320 Angle : 0.642 7.696 25370 Z= 0.334 Chirality : 0.045 0.207 2816 Planarity : 0.005 0.045 3112 Dihedral : 11.443 100.571 3003 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.72 % Allowed : 12.99 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: -0.98 (0.17), residues: 2176 helix: 0.59 (0.16), residues: 981 sheet: -1.37 (0.32), residues: 232 loop : -1.77 (0.18), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 270 TYR 0.024 0.002 TYR C 207 PHE 0.021 0.002 PHE A 132 TRP 0.026 0.002 TRP B 437 HIS 0.006 0.002 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00734 (18692) covalent geometry : angle 0.64220 (25370) hydrogen bonds : bond 0.04716 ( 819) hydrogen bonds : angle 4.45629 ( 2303) Misc. bond : bond 0.00195 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 135 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 TYR cc_start: 0.8559 (p90) cc_final: 0.8313 (p90) REVERT: A 243 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7937 (mp) REVERT: A 437 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8571 (tp30) REVERT: A 668 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8772 (tt) REVERT: B 562 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7796 (ttp80) REVERT: B 685 GLU cc_start: 0.7811 (tt0) cc_final: 0.7500 (tm-30) REVERT: C 233 MET cc_start: 0.9010 (tpp) cc_final: 0.8611 (tpp) REVERT: C 396 MET cc_start: 0.8176 (mtp) cc_final: 0.7901 (ptp) REVERT: C 423 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8734 (mp) REVERT: C 537 MET cc_start: 0.8929 (tmm) cc_final: 0.8641 (tmm) REVERT: C 584 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8458 (pp) REVERT: C 721 LYS cc_start: 0.8956 (mttt) cc_final: 0.8521 (ttpp) outliers start: 52 outliers final: 36 residues processed: 181 average time/residue: 0.1456 time to fit residues: 40.9715 Evaluate side-chains 172 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 562 ARG Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 527 GLN Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 689 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 209 optimal weight: 0.1980 chunk 212 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 168 optimal weight: 0.4980 chunk 91 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 174 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 388 GLN B 314 ASN B 382 ASN ** B 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.067030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.053622 restraints weight = 52119.041| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.55 r_work: 0.2834 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18693 Z= 0.096 Angle : 0.483 7.158 25370 Z= 0.250 Chirality : 0.039 0.207 2816 Planarity : 0.003 0.040 3112 Dihedral : 11.231 96.774 3002 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.04 % Allowed : 13.93 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.18), residues: 2176 helix: 1.16 (0.17), residues: 979 sheet: -1.41 (0.32), residues: 239 loop : -1.52 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 169 TYR 0.013 0.001 TYR A 644 PHE 0.010 0.001 PHE A 223 TRP 0.015 0.001 TRP B 437 HIS 0.002 0.000 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00212 (18692) covalent geometry : angle 0.48252 (25370) hydrogen bonds : bond 0.03326 ( 819) hydrogen bonds : angle 4.11234 ( 2303) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.9246 (tmm-80) cc_final: 0.9041 (tmm-80) REVERT: A 97 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7883 (mp10) REVERT: A 437 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8495 (tp30) REVERT: A 550 GLU cc_start: 0.8616 (tt0) cc_final: 0.8213 (tm-30) REVERT: B 98 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: B 562 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7594 (ttp80) REVERT: B 685 GLU cc_start: 0.7604 (tt0) cc_final: 0.7229 (tm-30) REVERT: B 740 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8271 (mp0) REVERT: C 233 MET cc_start: 0.8983 (tpp) cc_final: 0.8593 (tpp) REVERT: C 237 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9205 (mm) REVERT: C 381 MET cc_start: 0.8512 (mmm) cc_final: 0.8154 (mmm) REVERT: C 537 MET cc_start: 0.8673 (tmm) cc_final: 0.8433 (tmm) REVERT: C 721 LYS cc_start: 0.8957 (mttt) cc_final: 0.8491 (ttpp) outliers start: 39 outliers final: 27 residues processed: 177 average time/residue: 0.1587 time to fit residues: 42.6917 Evaluate side-chains 165 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 562 ARG Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain C residue 170 PHE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 527 GLN Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 689 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 160 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 173 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 ASN ** B 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.065945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.052496 restraints weight = 52384.573| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.55 r_work: 0.2805 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18693 Z= 0.157 Angle : 0.509 8.561 25370 Z= 0.263 Chirality : 0.040 0.198 2816 Planarity : 0.003 0.039 3112 Dihedral : 11.179 97.635 3002 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.41 % Allowed : 13.78 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: -0.34 (0.18), residues: 2176 helix: 1.22 (0.17), residues: 982 sheet: -1.34 (0.32), residues: 244 loop : -1.49 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 178 TYR 0.033 0.001 TYR A 154 PHE 0.011 0.001 PHE A 132 TRP 0.018 0.001 TRP B 437 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00357 (18692) covalent geometry : angle 0.50873 (25370) hydrogen bonds : bond 0.03631 ( 819) hydrogen bonds : angle 4.06914 ( 2303) Misc. bond : bond 0.00086 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 135 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ARG cc_start: 0.8375 (ptt-90) cc_final: 0.7876 (ptt-90) REVERT: A 437 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8468 (tp30) REVERT: A 668 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8670 (tt) REVERT: B 98 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7942 (tm-30) REVERT: B 206 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7387 (ppp) REVERT: B 562 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7659 (ttp80) REVERT: B 685 GLU cc_start: 0.7731 (tt0) cc_final: 0.7372 (tm-30) REVERT: B 740 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8310 (mp0) REVERT: C 43 LYS cc_start: 0.7963 (tttp) cc_final: 0.7512 (tttp) REVERT: C 233 MET cc_start: 0.8975 (tpp) cc_final: 0.8596 (tpp) REVERT: C 381 MET cc_start: 0.8598 (mmm) cc_final: 0.8198 (mmm) REVERT: C 396 MET cc_start: 0.8558 (ptp) cc_final: 0.8325 (ptp) REVERT: C 537 MET cc_start: 0.8752 (tmm) cc_final: 0.8536 (tmm) REVERT: C 584 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8346 (pp) REVERT: C 721 LYS cc_start: 0.8941 (mttt) cc_final: 0.8478 (ttpp) outliers start: 46 outliers final: 34 residues processed: 177 average time/residue: 0.1540 time to fit residues: 41.9752 Evaluate side-chains 173 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 562 ARG Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 527 GLN Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 689 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 212 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 218 optimal weight: 8.9990 chunk 217 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 2 optimal weight: 0.0050 chunk 193 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 HIS B 314 ASN ** B 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.067383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.054034 restraints weight = 52528.861| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.55 r_work: 0.2849 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18693 Z= 0.095 Angle : 0.468 6.888 25370 Z= 0.242 Chirality : 0.038 0.185 2816 Planarity : 0.003 0.039 3112 Dihedral : 11.086 94.883 3002 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.25 % Allowed : 13.93 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: -0.08 (0.18), residues: 2176 helix: 1.47 (0.17), residues: 985 sheet: -1.32 (0.31), residues: 254 loop : -1.35 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 7 TYR 0.025 0.001 TYR A 154 PHE 0.009 0.001 PHE B 7 TRP 0.014 0.001 TRP B 437 HIS 0.002 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00211 (18692) covalent geometry : angle 0.46826 (25370) hydrogen bonds : bond 0.03143 ( 819) hydrogen bonds : angle 3.93439 ( 2303) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7264 (mp10) REVERT: A 544 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9114 (tp) REVERT: B 98 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7926 (tm-30) REVERT: B 206 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7345 (ppp) REVERT: B 562 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7597 (ttp80) REVERT: B 685 GLU cc_start: 0.7687 (tt0) cc_final: 0.7311 (tm-30) REVERT: B 740 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8292 (mp0) REVERT: C 43 LYS cc_start: 0.7898 (tttp) cc_final: 0.7399 (tttp) REVERT: C 233 MET cc_start: 0.8894 (tpp) cc_final: 0.8566 (tpp) REVERT: C 381 MET cc_start: 0.8529 (mmm) cc_final: 0.8138 (mmm) REVERT: C 396 MET cc_start: 0.8501 (ptp) cc_final: 0.8155 (ptp) REVERT: C 584 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8345 (pp) REVERT: C 721 LYS cc_start: 0.8949 (mttt) cc_final: 0.8450 (ttpp) outliers start: 43 outliers final: 28 residues processed: 178 average time/residue: 0.1569 time to fit residues: 42.8806 Evaluate side-chains 165 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 562 ARG Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 170 PHE Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 527 GLN Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 584 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 17 optimal weight: 7.9990 chunk 216 optimal weight: 0.0050 chunk 151 optimal weight: 0.5980 chunk 201 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 175 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 ASN ** B 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.068773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.055961 restraints weight = 52291.092| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.37 r_work: 0.2928 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18693 Z= 0.088 Angle : 0.471 7.530 25370 Z= 0.239 Chirality : 0.038 0.169 2816 Planarity : 0.003 0.039 3112 Dihedral : 11.016 92.861 2999 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.99 % Allowed : 14.72 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: 0.06 (0.18), residues: 2176 helix: 1.57 (0.17), residues: 994 sheet: -1.27 (0.31), residues: 259 loop : -1.27 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 7 TYR 0.021 0.001 TYR A 154 PHE 0.008 0.001 PHE B 7 TRP 0.013 0.001 TRP B 437 HIS 0.003 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00196 (18692) covalent geometry : angle 0.47072 (25370) hydrogen bonds : bond 0.03018 ( 819) hydrogen bonds : angle 3.82772 ( 2303) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7332 (mp10) REVERT: A 544 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9103 (tp) REVERT: B 206 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7463 (ppp) REVERT: B 562 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7756 (ttp80) REVERT: B 685 GLU cc_start: 0.7684 (tt0) cc_final: 0.7449 (tm-30) REVERT: C 43 LYS cc_start: 0.7815 (tttp) cc_final: 0.7359 (tttp) REVERT: C 233 MET cc_start: 0.8955 (tpp) cc_final: 0.8685 (tpp) REVERT: C 381 MET cc_start: 0.8333 (mmm) cc_final: 0.8040 (mmm) REVERT: C 396 MET cc_start: 0.8422 (ptp) cc_final: 0.8091 (ptp) REVERT: C 584 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8507 (pp) REVERT: C 721 LYS cc_start: 0.8874 (mttt) cc_final: 0.8526 (ttpp) outliers start: 38 outliers final: 30 residues processed: 169 average time/residue: 0.1541 time to fit residues: 39.8510 Evaluate side-chains 165 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 562 ARG Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 170 PHE Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 527 GLN Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 689 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 200 optimal weight: 6.9990 chunk 218 optimal weight: 8.9990 chunk 164 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 129 optimal weight: 7.9990 chunk 201 optimal weight: 0.9990 chunk 204 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 11 optimal weight: 0.0670 chunk 55 optimal weight: 7.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.065650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.052775 restraints weight = 53050.741| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.37 r_work: 0.2844 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 18693 Z= 0.246 Angle : 0.587 10.836 25370 Z= 0.300 Chirality : 0.043 0.223 2816 Planarity : 0.004 0.037 3112 Dihedral : 11.143 98.951 2998 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.15 % Allowed : 14.61 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.18), residues: 2176 helix: 1.28 (0.17), residues: 990 sheet: -1.23 (0.31), residues: 252 loop : -1.37 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 7 TYR 0.023 0.002 TYR A 154 PHE 0.016 0.002 PHE A 132 TRP 0.023 0.002 TRP B 437 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00561 (18692) covalent geometry : angle 0.58746 (25370) hydrogen bonds : bond 0.04091 ( 819) hydrogen bonds : angle 4.12121 ( 2303) Misc. bond : bond 0.00129 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8196 (mp) REVERT: A 376 MET cc_start: 0.8198 (mmp) cc_final: 0.7943 (mmt) REVERT: A 668 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8810 (tt) REVERT: B 206 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7514 (ppp) REVERT: B 562 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7864 (ttp80) REVERT: C 43 LYS cc_start: 0.8002 (tttp) cc_final: 0.7597 (tttp) REVERT: C 233 MET cc_start: 0.9002 (tpp) cc_final: 0.8707 (tpp) REVERT: C 396 MET cc_start: 0.8454 (ptp) cc_final: 0.8071 (ptp) REVERT: C 441 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8621 (tm) REVERT: C 584 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8537 (pp) REVERT: C 721 LYS cc_start: 0.8884 (mttt) cc_final: 0.8499 (ttpp) outliers start: 41 outliers final: 31 residues processed: 166 average time/residue: 0.1533 time to fit residues: 39.3931 Evaluate side-chains 163 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 562 ARG Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 527 GLN Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 689 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 115 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 208 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 203 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.067349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.054536 restraints weight = 52665.366| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.30 r_work: 0.2889 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18693 Z= 0.127 Angle : 0.517 7.618 25370 Z= 0.265 Chirality : 0.040 0.172 2816 Planarity : 0.003 0.038 3112 Dihedral : 11.051 98.034 2996 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.04 % Allowed : 14.72 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.18), residues: 2176 helix: 1.43 (0.17), residues: 992 sheet: -1.22 (0.33), residues: 227 loop : -1.26 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 7 TYR 0.026 0.001 TYR A 154 PHE 0.011 0.001 PHE B 7 TRP 0.016 0.001 TRP B 437 HIS 0.005 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00290 (18692) covalent geometry : angle 0.51684 (25370) hydrogen bonds : bond 0.03511 ( 819) hydrogen bonds : angle 3.99635 ( 2303) Misc. bond : bond 0.00054 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8229 (mp) REVERT: B 206 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7455 (ppp) REVERT: B 562 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7751 (ttp80) REVERT: C 43 LYS cc_start: 0.7824 (tttp) cc_final: 0.7383 (tttp) REVERT: C 49 MET cc_start: 0.9124 (tpt) cc_final: 0.8811 (tpt) REVERT: C 233 MET cc_start: 0.8999 (tpp) cc_final: 0.8714 (tpp) REVERT: C 381 MET cc_start: 0.8421 (mmm) cc_final: 0.8132 (mmm) REVERT: C 441 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8603 (tm) REVERT: C 584 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8537 (pp) REVERT: C 721 LYS cc_start: 0.8864 (mttt) cc_final: 0.8494 (ttpp) outliers start: 39 outliers final: 30 residues processed: 160 average time/residue: 0.1550 time to fit residues: 38.1430 Evaluate side-chains 159 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 562 ARG Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 527 GLN Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 689 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 88 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 54 optimal weight: 0.0670 chunk 160 optimal weight: 0.0980 chunk 44 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 overall best weight: 0.4720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.068898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.056178 restraints weight = 52169.229| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.35 r_work: 0.2938 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18693 Z= 0.087 Angle : 0.493 10.569 25370 Z= 0.251 Chirality : 0.038 0.158 2816 Planarity : 0.003 0.040 3112 Dihedral : 10.975 93.854 2996 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.73 % Allowed : 14.93 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.18), residues: 2176 helix: 1.60 (0.17), residues: 995 sheet: -1.02 (0.34), residues: 224 loop : -1.16 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 397 TYR 0.024 0.001 TYR A 154 PHE 0.008 0.001 PHE A 223 TRP 0.012 0.001 TRP A 695 HIS 0.004 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00191 (18692) covalent geometry : angle 0.49317 (25370) hydrogen bonds : bond 0.03054 ( 819) hydrogen bonds : angle 3.84707 ( 2303) Misc. bond : bond 0.00004 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4649.42 seconds wall clock time: 80 minutes 41.70 seconds (4841.70 seconds total)