Starting phenix.real_space_refine on Sat Jul 4 05:19:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qtl_14144/07_2026/7qtl_14144.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qtl_14144/07_2026/7qtl_14144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7qtl_14144/07_2026/7qtl_14144.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qtl_14144/07_2026/7qtl_14144.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qtl_14144/07_2026/7qtl_14144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qtl_14144/07_2026/7qtl_14144.map" model { file = "/net/cci-nas-00/data/ceres_data/7qtl_14144/07_2026/7qtl_14144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qtl_14144/07_2026/7qtl_14144.cif" } resolution = 2.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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 50 5.49 5 Mg 2 5.21 5 S 126 5.16 5 C 11329 2.51 5 N 3199 2.21 5 O 3691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18397 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 5755 Classifications: {'peptide': 709} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 676} Chain breaks: 1 Chain: "B" Number of atoms: 5736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 717, 5728 Classifications: {'peptide': 717} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 686} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 717, 5728 Classifications: {'peptide': 717} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 686} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 5829 Chain: "C" Number of atoms: 5767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5767 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 29, 'TRANS': 696} Chain breaks: 2 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': 2, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 9} Chain: "R" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 9} Link IDs: {'rna2p': 2, 'rna3p': 11} Chain: "M" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 365 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 9, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 14} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 2, '2TM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'GTA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "V" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "M" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALEU B 218 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU B 218 " occ=0.50 Time building chain proxies: 4.99, per 1000 atoms: 0.27 Number of scatterers: 18397 At special positions: 0 Unit cell: (117.029, 126.781, 122.718, 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 126 16.00 P 50 15.00 Mg 2 11.99 O 3691 8.00 N 3199 7.00 C 11329 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: 1.48 Conformation dependent library (CDL) restraints added in 823.8 milliseconds 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4054 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 24 sheets defined 51.1% alpha, 13.8% beta 10 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 0 through 9 Processing helix chain 'A' and resid 10 through 24 removed outlier: 4.143A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 50 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 139 removed outlier: 3.561A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 185 removed outlier: 3.586A pdb=" N ARG A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 193 removed outlier: 3.775A pdb=" N PHE A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 302 through 313 removed outlier: 3.580A pdb=" N ASP A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.710A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 385 removed outlier: 3.500A pdb=" N CYS A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.552A pdb=" N SER A 409 " --> pdb=" O CYS A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 452 removed outlier: 3.869A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.976A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'A' and resid 582 through 604 removed outlier: 3.914A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 4.173A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 697 through 716 removed outlier: 3.710A pdb=" N ARG A 716 " --> pdb=" O THR A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 5.877A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.520A pdb=" N SER B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.502A pdb=" N GLY B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 174 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 265 removed outlier: 4.168A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 293 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.868A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.758A pdb=" N TYR B 380 " --> pdb=" O ASP B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 473 removed outlier: 3.536A pdb=" N VAL B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 512 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 678 through 680 No H-bonds generated for 'chain 'B' and resid 678 through 680' Processing helix chain 'B' and resid 681 through 700 removed outlier: 4.025A pdb=" N ASP B 685 " --> pdb=" O GLY B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 733 Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.797A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 22 Processing helix chain 'C' and resid 24 through 34 removed outlier: 3.998A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 62 through 66 Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.805A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 169 through 172 removed outlier: 3.845A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 251 through 273 removed outlier: 4.118A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER C 273 " --> pdb=" O ARG C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 294 through 299 Processing helix chain 'C' and resid 305 through 315 Processing helix chain 'C' and resid 390 through 406 removed outlier: 3.759A pdb=" N GLN C 406 " --> pdb=" O MET C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 429 through 441 removed outlier: 3.639A pdb=" N LYS C 440 " --> pdb=" O ARG C 436 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP C 441 " --> pdb=" O HIS C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 450 removed outlier: 4.273A pdb=" N GLY C 450 " --> pdb=" O PHE C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 518 Processing helix chain 'C' and resid 541 through 556 Processing helix chain 'C' and resid 556 through 567 removed outlier: 3.819A pdb=" N SER C 565 " --> pdb=" O LYS C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 573 Processing helix chain 'C' and resid 574 through 576 No H-bonds generated for 'chain 'C' and resid 574 through 576' Processing helix chain 'C' and resid 577 through 582 Processing helix chain 'C' and resid 585 through 587 No H-bonds generated for 'chain 'C' and resid 585 through 587' Processing helix chain 'C' and resid 588 through 606 removed outlier: 3.814A pdb=" N VAL C 606 " --> pdb=" O GLN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 619 Processing helix chain 'C' and resid 620 through 624 removed outlier: 4.315A pdb=" N ALA C 624 " --> pdb=" O PHE C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 705 removed outlier: 3.609A pdb=" N GLY C 705 " --> pdb=" O LYS C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 713 removed outlier: 3.564A pdb=" N LEU C 713 " --> pdb=" O ILE C 710 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 292 removed outlier: 7.254A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL A 557 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU A 549 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 542 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY A 546 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLU A 319 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N MET A 548 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N TRP A 317 " --> pdb=" O MET A 548 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 292 removed outlier: 5.378A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 378 removed outlier: 5.794A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 627 through 631 removed outlier: 6.104A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (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 182 Processing sheet with id=AB2, first strand: chain 'B' and resid 240 through 244 removed outlier: 3.885A pdb=" N THR B 226 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB4, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.359A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 135 removed outlier: 4.755A pdb=" N MET C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.724A pdb=" N LYS C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 292 through 293 Processing sheet with id=AB8, first strand: chain 'C' and resid 323 through 325 removed outlier: 6.817A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA C 377 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LEU C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N ARG C 479 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU C 384 " --> pdb=" O ARG C 479 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 338 through 345 Processing sheet with id=AC1, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AC2, first strand: chain 'C' and resid 462 through 463 Processing sheet with id=AC3, first strand: chain 'C' and resid 504 through 505 removed outlier: 6.733A pdb=" N VAL C 504 " --> pdb=" O LEU C 512 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 635 through 640 Processing sheet with id=AC5, first strand: chain 'C' and resid 657 through 658 removed outlier: 6.339A pdb=" N LEU C 665 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 687 through 691 removed outlier: 5.690A pdb=" N ALA C 689 " --> pdb=" O PHE C 694 " (cutoff:3.500A) removed outlier: 9.437A pdb=" N PHE C 694 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU C 733 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU C 720 " --> pdb=" O LYS C 736 " (cutoff:3.500A) 890 hydrogen bonds defined for protein. 2452 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 3.78 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5716 1.34 - 1.46: 3420 1.46 - 1.58: 9266 1.58 - 1.70: 94 1.70 - 1.82: 222 Bond restraints: 18718 Sorted by residual: bond pdb=" O3B 2TM B 901 " pdb=" PG 2TM B 901 " ideal model delta sigma weight residual 1.700 1.610 0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C5 GTA M 101 " pdb=" C6 GTA M 101 " ideal model delta sigma weight residual 1.422 1.336 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C5C GTA M 101 " pdb=" C6C GTA M 101 " ideal model delta sigma weight residual 1.404 1.329 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C2C GTA M 101 " pdb=" N3C GTA M 101 " ideal model delta sigma weight residual 1.322 1.396 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C1B GTA M 101 " pdb=" O4B GTA M 101 " ideal model delta sigma weight residual 1.395 1.463 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 18713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 25040 2.07 - 4.15: 348 4.15 - 6.22: 55 6.22 - 8.29: 16 8.29 - 10.36: 4 Bond angle restraints: 25463 Sorted by residual: angle pdb=" N PRO A 28 " pdb=" CD PRO A 28 " pdb=" CG PRO A 28 " ideal model delta sigma weight residual 103.20 97.43 5.77 1.50e+00 4.44e-01 1.48e+01 angle pdb=" CA GLU A 243 " pdb=" CB GLU A 243 " pdb=" CG GLU A 243 " ideal model delta sigma weight residual 114.10 121.74 -7.64 2.00e+00 2.50e-01 1.46e+01 angle pdb=" O3' A M 8 " pdb=" C3' A M 8 " pdb=" C2' A M 8 " ideal model delta sigma weight residual 113.70 119.10 -5.40 1.50e+00 4.44e-01 1.30e+01 angle pdb=" N1C GTA M 101 " pdb=" C2C GTA M 101 " pdb=" N3C GTA M 101 " ideal model delta sigma weight residual 128.44 118.08 10.36 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C5 GTA M 101 " pdb=" C6 GTA M 101 " pdb=" N1 GTA M 101 " ideal model delta sigma weight residual 109.94 119.90 -9.96 3.00e+00 1.11e-01 1.10e+01 ... (remaining 25458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 10975 35.83 - 71.66: 394 71.66 - 107.49: 43 107.49 - 143.32: 3 143.32 - 179.15: 2 Dihedral angle restraints: 11417 sinusoidal: 5159 harmonic: 6258 Sorted by residual: dihedral pdb=" CD ARG B 287 " pdb=" NE ARG B 287 " pdb=" CZ ARG B 287 " pdb=" NH1 ARG B 287 " ideal model delta sinusoidal sigma weight residual 0.00 60.23 -60.23 1 1.00e+01 1.00e-02 4.83e+01 dihedral pdb=" CA VAL C 220 " pdb=" C VAL C 220 " pdb=" N ALA C 221 " pdb=" CA ALA C 221 " ideal model delta harmonic sigma weight residual 180.00 158.53 21.47 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA GLU A 352 " pdb=" C GLU A 352 " pdb=" N LYS A 353 " pdb=" CA LYS A 353 " ideal model delta harmonic sigma weight residual 180.00 159.27 20.73 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 11414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2411 0.058 - 0.115: 387 0.115 - 0.173: 38 0.173 - 0.230: 3 0.230 - 0.288: 2 Chirality restraints: 2841 Sorted by residual: chirality pdb=" C3' A M 8 " pdb=" C4' A M 8 " pdb=" O3' A M 8 " pdb=" C2' A M 8 " both_signs ideal model delta sigma weight residual False -2.48 -2.19 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C4B GTA M 101 " pdb=" C3B GTA M 101 " pdb=" C5B GTA M 101 " pdb=" O4B GTA M 101 " both_signs ideal model delta sigma weight residual False -2.53 -2.77 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C1A GTA M 101 " pdb=" C2A GTA M 101 " pdb=" N9 GTA M 101 " pdb=" O4A GTA M 101 " both_signs ideal model delta sigma weight residual False 2.37 2.57 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2838 not shown) Planarity restraints: 3108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 287 " 0.753 9.50e-02 1.11e+02 3.39e-01 8.54e+01 pdb=" NE ARG B 287 " -0.070 2.00e-02 2.50e+03 pdb=" CZ ARG B 287 " 0.060 2.00e-02 2.50e+03 pdb=" NH1 ARG B 287 " -0.022 2.00e-02 2.50e+03 pdb=" NH2 ARG B 287 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 582 " 0.015 2.00e-02 2.50e+03 3.10e-02 9.58e+00 pdb=" C ARG A 582 " -0.054 2.00e-02 2.50e+03 pdb=" O ARG A 582 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG A 583 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 653 " -0.048 5.00e-02 4.00e+02 7.24e-02 8.40e+00 pdb=" N PRO C 654 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 654 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 654 " -0.040 5.00e-02 4.00e+02 ... (remaining 3105 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 195 2.57 - 3.15: 14391 3.15 - 3.74: 30443 3.74 - 4.32: 44504 4.32 - 4.90: 70164 Nonbonded interactions: 159697 Sorted by model distance: nonbonded pdb="MG MG B 902 " pdb=" O HOH B1015 " model vdw 1.988 2.170 nonbonded pdb="MG MG B 903 " pdb=" O HOH B1025 " model vdw 2.033 2.170 nonbonded pdb=" OD1 ASN C 301 " pdb=" OG1 THR C 303 " model vdw 2.120 3.040 nonbonded pdb=" OD2 ASP B 41 " pdb=" NH1 ARG B 45 " model vdw 2.131 3.120 nonbonded pdb=" OE1 GLU A 524 " pdb=" O HOH A 801 " model vdw 2.140 3.040 ... (remaining 159692 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 11.140 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.100 Find NCS groups from input model: 0.170 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:5.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 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 : 0.004 0.090 18719 Z= 0.184 Angle : 0.645 10.363 25463 Z= 0.327 Chirality : 0.042 0.288 2841 Planarity : 0.008 0.339 3108 Dihedral : 17.617 179.147 7363 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.39 % Favored : 97.56 % Rotamer: Outliers : 3.98 % Allowed : 19.70 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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 are not related in a simple way. whole: -1.53 (0.16), residues: 2137 helix: -0.37 (0.15), residues: 984 sheet: -1.02 (0.33), residues: 222 loop : -1.65 (0.18), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.069 0.001 ARG B 287 TYR 0.015 0.002 TYR A 48 PHE 0.015 0.001 PHE B 551 TRP 0.016 0.002 TRP A 368 HIS 0.004 0.001 HIS B 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (18718) covalent geometry : angle 0.64487 / 0.33 (25463) hydrogen bonds : bond 0.12934 / 8.68 ( 911) hydrogen bonds : angle 5.83378 / 4.20 ( 2502) Misc. bond : bond 0.04513 / 2.82 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 241 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 411 MET cc_start: 0.8619 (mmp) cc_final: 0.8137 (mmp) REVERT: C 171 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7634 (mm-30) outliers start: 76 outliers final: 20 residues processed: 303 average time/residue: 0.8118 time to fit residues: 268.8311 Evaluate side-chains 180 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 711 ASN Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0870 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 0.0030 chunk 77 optimal weight: 0.7980 overall best weight: 0.3766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS A 146 HIS A 388 ASN A 556 GLN B 115 GLN B 532 ASN C 75 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.084852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.067515 restraints weight = 57861.785| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.39 r_work: 0.3025 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (15 function evaluations) r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 18719 Z= 0.117 Angle : 0.540 9.097 25463 Z= 0.286 Chirality : 0.040 0.196 2841 Planarity : 0.004 0.052 3108 Dihedral : 10.352 178.108 3005 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.46 % Allowed : 20.38 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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 are not related in a simple way. whole: -0.15 (0.17), residues: 2137 helix: 0.97 (0.16), residues: 991 sheet: -0.51 (0.35), residues: 215 loop : -1.15 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 45 TYR 0.013 0.001 TYR C 115 PHE 0.016 0.001 PHE A 4 TRP 0.011 0.001 TRP A 368 HIS 0.002 0.000 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (18718) covalent geometry : angle 0.53983 / 0.29 (25463) hydrogen bonds : bond 0.04164 / 2.78 ( 911) hydrogen bonds : angle 4.62223 / 3.32 ( 2502) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 HIS cc_start: 0.8196 (t70) cc_final: 0.7900 (t-90) REVERT: C 171 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8129 (mm-30) REVERT: C 217 PHE cc_start: 0.9423 (OUTLIER) cc_final: 0.9192 (m-80) REVERT: C 294 MET cc_start: 0.9113 (ttt) cc_final: 0.8732 (ttt) REVERT: C 361 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8322 (mt-10) REVERT: C 473 MET cc_start: 0.8063 (tpp) cc_final: 0.7727 (mmt) outliers start: 47 outliers final: 16 residues processed: 218 average time/residue: 0.7418 time to fit residues: 178.3687 Evaluate side-chains 169 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 715 ASN Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 82 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 184 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN B 562 HIS B 567 GLN B 694 ASN C 42 ASN C 75 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.081978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.064987 restraints weight = 58187.975| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.28 r_work: 0.2979 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18719 Z= 0.202 Angle : 0.561 6.322 25463 Z= 0.297 Chirality : 0.042 0.198 2841 Planarity : 0.004 0.041 3108 Dihedral : 10.058 179.655 2981 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.62 % Allowed : 20.01 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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 are not related in a simple way. whole: 0.22 (0.18), residues: 2137 helix: 1.22 (0.16), residues: 1000 sheet: -0.31 (0.34), residues: 233 loop : -0.93 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 75 TYR 0.023 0.002 TYR A 48 PHE 0.015 0.002 PHE A 4 TRP 0.013 0.002 TRP A 422 HIS 0.003 0.001 HIS B 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (18718) covalent geometry : angle 0.56087 / 0.30 (25463) hydrogen bonds : bond 0.04853 / 3.23 ( 911) hydrogen bonds : angle 4.60780 / 3.30 ( 2502) Misc. bond : bond 0.00104 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 157 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 HIS cc_start: 0.8260 (t70) cc_final: 0.8054 (t70) REVERT: A 346 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.8109 (tp40) REVERT: B 227 MET cc_start: 0.8881 (mpp) cc_final: 0.8665 (mpp) REVERT: B 636 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7963 (tp30) REVERT: C 70 ARG cc_start: 0.8367 (ttm-80) cc_final: 0.8002 (mtt-85) REVERT: C 217 PHE cc_start: 0.9459 (OUTLIER) cc_final: 0.9182 (m-80) outliers start: 50 outliers final: 24 residues processed: 193 average time/residue: 0.7700 time to fit residues: 163.5593 Evaluate side-chains 170 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 569 GLN Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 703 ARG Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 213 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 191 optimal weight: 0.0870 chunk 99 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 97 optimal weight: 0.0570 chunk 2 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.8278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN C 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.082975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.065874 restraints weight = 68320.256| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.48 r_work: 0.2997 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18719 Z= 0.133 Angle : 0.523 9.609 25463 Z= 0.276 Chirality : 0.040 0.193 2841 Planarity : 0.004 0.040 3108 Dihedral : 9.776 178.895 2977 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.20 % Allowed : 20.64 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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 are not related in a simple way. whole: 0.47 (0.18), residues: 2137 helix: 1.45 (0.16), residues: 999 sheet: -0.19 (0.34), residues: 230 loop : -0.81 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 287 TYR 0.020 0.001 TYR A 48 PHE 0.017 0.001 PHE A 4 TRP 0.013 0.001 TRP C 49 HIS 0.002 0.001 HIS C 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (18718) covalent geometry : angle 0.52314 / 0.28 (25463) hydrogen bonds : bond 0.04190 / 2.79 ( 911) hydrogen bonds : angle 4.45836 / 3.19 ( 2502) Misc. bond : bond 0.00064 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8102 (tp40) REVERT: B 655 MET cc_start: 0.8294 (mmm) cc_final: 0.8075 (mmt) REVERT: C 70 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.7935 (mtt-85) REVERT: C 294 MET cc_start: 0.9115 (ttt) cc_final: 0.8708 (ttt) REVERT: C 361 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8367 (mt-10) REVERT: C 473 MET cc_start: 0.7529 (mmt) cc_final: 0.7311 (mmp) REVERT: C 508 ARG cc_start: 0.8820 (mpp80) cc_final: 0.8455 (mpp80) outliers start: 42 outliers final: 17 residues processed: 184 average time/residue: 0.7208 time to fit residues: 146.1414 Evaluate side-chains 161 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 715 ASN Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 187 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 193 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 HIS C 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.081310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.064560 restraints weight = 63225.784| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.35 r_work: 0.2978 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18719 Z= 0.185 Angle : 0.555 7.927 25463 Z= 0.292 Chirality : 0.042 0.192 2841 Planarity : 0.004 0.041 3108 Dihedral : 9.790 179.719 2975 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.78 % Allowed : 20.12 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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 are not related in a simple way. whole: 0.53 (0.18), residues: 2137 helix: 1.47 (0.16), residues: 1003 sheet: -0.17 (0.34), residues: 232 loop : -0.77 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 630 TYR 0.024 0.002 TYR A 48 PHE 0.017 0.001 PHE C 694 TRP 0.013 0.001 TRP A 422 HIS 0.003 0.001 HIS C 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (18718) covalent geometry : angle 0.55538 / 0.29 (25463) hydrogen bonds : bond 0.04632 / 3.07 ( 911) hydrogen bonds : angle 4.50848 / 3.22 ( 2502) Misc. bond : bond 0.00109 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 149 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8428 (mm110) cc_final: 0.7804 (pt0) REVERT: A 346 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8105 (tp40) REVERT: C 51 MET cc_start: 0.8619 (mmm) cc_final: 0.8353 (tpt) REVERT: C 70 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8022 (mtt-85) REVERT: C 361 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8353 (mt-10) REVERT: C 443 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8822 (mtpt) REVERT: C 700 GLU cc_start: 0.8499 (tt0) cc_final: 0.8241 (mm-30) outliers start: 52 outliers final: 25 residues processed: 190 average time/residue: 0.7037 time to fit residues: 148.0923 Evaluate side-chains 171 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 443 LYS Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain C residue 715 ASN Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 163 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 132 optimal weight: 0.0000 chunk 137 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 173 optimal weight: 0.5980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 HIS A 388 ASN C 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.082971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.066551 restraints weight = 58198.023| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.27 r_work: 0.3029 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18719 Z= 0.115 Angle : 0.508 8.623 25463 Z= 0.267 Chirality : 0.039 0.184 2841 Planarity : 0.004 0.051 3108 Dihedral : 9.589 179.968 2975 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.51 % Allowed : 20.12 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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 are not related in a simple way. whole: 0.76 (0.18), residues: 2137 helix: 1.68 (0.16), residues: 996 sheet: -0.04 (0.36), residues: 223 loop : -0.65 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 368 TYR 0.019 0.001 TYR A 48 PHE 0.015 0.001 PHE C 694 TRP 0.014 0.001 TRP C 49 HIS 0.001 0.001 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (18718) covalent geometry : angle 0.50797 / 0.27 (25463) hydrogen bonds : bond 0.03934 / 2.61 ( 911) hydrogen bonds : angle 4.36414 / 3.12 ( 2502) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 149 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8376 (mm110) cc_final: 0.7828 (pt0) REVERT: A 346 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.8090 (tp40) REVERT: C 70 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7951 (mtt-85) REVERT: C 294 MET cc_start: 0.9090 (ttt) cc_final: 0.8669 (ttt) REVERT: C 369 ARG cc_start: 0.8953 (mtm-85) cc_final: 0.8410 (mtm-85) REVERT: C 461 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7858 (tt) REVERT: C 700 GLU cc_start: 0.8483 (tt0) cc_final: 0.8231 (mm-30) outliers start: 47 outliers final: 23 residues processed: 186 average time/residue: 0.7212 time to fit residues: 148.0605 Evaluate side-chains 166 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 166 optimal weight: 4.9990 chunk 204 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 170 optimal weight: 0.0670 chunk 15 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 HIS C 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.083013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.066295 restraints weight = 68340.714| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.45 r_work: 0.3018 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18719 Z= 0.118 Angle : 0.520 11.419 25463 Z= 0.270 Chirality : 0.040 0.180 2841 Planarity : 0.003 0.041 3108 Dihedral : 9.527 179.499 2975 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.10 % Allowed : 20.69 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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 are not related in a simple way. whole: 0.88 (0.18), residues: 2137 helix: 1.76 (0.16), residues: 996 sheet: 0.08 (0.34), residues: 239 loop : -0.59 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 754 TYR 0.019 0.001 TYR A 48 PHE 0.015 0.001 PHE C 694 TRP 0.014 0.001 TRP C 49 HIS 0.002 0.001 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (18718) covalent geometry : angle 0.52032 / 0.27 (25463) hydrogen bonds : bond 0.03908 / 2.59 ( 911) hydrogen bonds : angle 4.32255 / 3.09 ( 2502) Misc. bond : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 144 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8135 (tp40) REVERT: B 655 MET cc_start: 0.8354 (mmm) cc_final: 0.8123 (mmt) REVERT: C 51 MET cc_start: 0.8522 (mmm) cc_final: 0.8253 (tpt) REVERT: C 53 MET cc_start: 0.7797 (mtt) cc_final: 0.7574 (mtp) REVERT: C 64 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8437 (mmm) REVERT: C 70 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7946 (mtt-85) REVERT: C 294 MET cc_start: 0.9084 (ttt) cc_final: 0.8673 (ttt) REVERT: C 369 ARG cc_start: 0.9018 (mtm-85) cc_final: 0.8491 (mtm-85) REVERT: C 461 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7902 (tt) outliers start: 39 outliers final: 23 residues processed: 173 average time/residue: 0.7006 time to fit residues: 134.0420 Evaluate side-chains 165 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 1 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 56 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 115 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 HIS C 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.082944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.066354 restraints weight = 63500.010| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.38 r_work: 0.3022 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18719 Z= 0.124 Angle : 0.525 10.761 25463 Z= 0.273 Chirality : 0.040 0.177 2841 Planarity : 0.004 0.065 3108 Dihedral : 9.488 179.010 2975 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.15 % Allowed : 20.74 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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 are not related in a simple way. whole: 0.92 (0.18), residues: 2137 helix: 1.79 (0.16), residues: 996 sheet: 0.18 (0.34), residues: 238 loop : -0.59 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 368 TYR 0.021 0.001 TYR A 305 PHE 0.014 0.001 PHE C 694 TRP 0.013 0.001 TRP C 49 HIS 0.002 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (18718) covalent geometry : angle 0.52515 / 0.27 (25463) hydrogen bonds : bond 0.03935 / 2.60 ( 911) hydrogen bonds : angle 4.31679 / 3.08 ( 2502) Misc. bond : bond 0.00041 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: A 129 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8300 (mm) REVERT: A 346 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8117 (tp40) REVERT: B 655 MET cc_start: 0.8404 (mmm) cc_final: 0.8161 (mmt) REVERT: C 51 MET cc_start: 0.8538 (mmm) cc_final: 0.8300 (tpt) REVERT: C 70 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7940 (mtt-85) REVERT: C 294 MET cc_start: 0.9087 (ttt) cc_final: 0.8684 (ttt) REVERT: C 369 ARG cc_start: 0.8939 (mtm-85) cc_final: 0.8382 (mtm-85) REVERT: C 461 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7852 (tt) REVERT: C 508 ARG cc_start: 0.8904 (mpp80) cc_final: 0.8644 (mpp80) outliers start: 40 outliers final: 20 residues processed: 172 average time/residue: 0.7083 time to fit residues: 134.7904 Evaluate side-chains 162 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 211 optimal weight: 0.0770 chunk 23 optimal weight: 0.5980 chunk 186 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 197 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 HIS C 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.083286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.066652 restraints weight = 61228.925| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.33 r_work: 0.3026 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18719 Z= 0.116 Angle : 0.527 10.453 25463 Z= 0.271 Chirality : 0.039 0.173 2841 Planarity : 0.004 0.048 3108 Dihedral : 9.377 178.445 2971 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.73 % Allowed : 21.06 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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 are not related in a simple way. whole: 0.98 (0.18), residues: 2137 helix: 1.82 (0.16), residues: 996 sheet: 0.24 (0.34), residues: 238 loop : -0.54 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 57 TYR 0.013 0.001 TYR A 48 PHE 0.013 0.001 PHE C 694 TRP 0.015 0.001 TRP C 49 HIS 0.002 0.000 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (18718) covalent geometry : angle 0.52722 / 0.27 (25463) hydrogen bonds : bond 0.03822 / 2.53 ( 911) hydrogen bonds : angle 4.28272 / 3.05 ( 2502) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 346 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8086 (tp40) REVERT: C 53 MET cc_start: 0.7926 (mtt) cc_final: 0.7698 (mtp) REVERT: C 70 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7940 (mtt-85) REVERT: C 294 MET cc_start: 0.9090 (ttt) cc_final: 0.8675 (ttt) REVERT: C 339 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8550 (mtmp) REVERT: C 369 ARG cc_start: 0.8998 (mtm-85) cc_final: 0.8459 (mtm-85) REVERT: C 461 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7837 (tt) REVERT: C 508 ARG cc_start: 0.8908 (mpp80) cc_final: 0.8643 (mpp80) outliers start: 32 outliers final: 20 residues processed: 169 average time/residue: 0.6738 time to fit residues: 125.7250 Evaluate side-chains 163 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 339 LYS Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 19 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 HIS C 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.082083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.065429 restraints weight = 58831.782| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.29 r_work: 0.2999 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18719 Z= 0.156 Angle : 0.568 11.947 25463 Z= 0.291 Chirality : 0.041 0.176 2841 Planarity : 0.004 0.098 3108 Dihedral : 9.431 177.938 2971 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.73 % Allowed : 21.27 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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 are not related in a simple way. whole: 0.92 (0.18), residues: 2137 helix: 1.75 (0.16), residues: 1000 sheet: 0.22 (0.35), residues: 233 loop : -0.56 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG C 368 TYR 0.024 0.001 TYR A 305 PHE 0.013 0.001 PHE A 4 TRP 0.011 0.001 TRP C 49 HIS 0.002 0.001 HIS C 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (18718) covalent geometry : angle 0.56828 / 0.29 (25463) hydrogen bonds : bond 0.04221 / 2.79 ( 911) hydrogen bonds : angle 4.37641 / 3.13 ( 2502) Misc. bond : bond 0.00069 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 346 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8070 (tp40) REVERT: C 70 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7957 (mtt-85) REVERT: C 461 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7968 (tt) REVERT: C 508 ARG cc_start: 0.8908 (mpp80) cc_final: 0.8642 (mpp80) outliers start: 32 outliers final: 18 residues processed: 165 average time/residue: 0.6827 time to fit residues: 125.2267 Evaluate side-chains 161 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 140 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 chunk 214 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 HIS C 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.081828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.065577 restraints weight = 50203.250| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.09 r_work: 0.3009 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18719 Z= 0.163 Angle : 0.577 12.377 25463 Z= 0.294 Chirality : 0.041 0.177 2841 Planarity : 0.004 0.051 3108 Dihedral : 9.442 177.494 2971 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.57 % Allowed : 21.32 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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 are not related in a simple way. whole: 0.90 (0.18), residues: 2137 helix: 1.74 (0.16), residues: 999 sheet: 0.13 (0.34), residues: 241 loop : -0.54 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 57 TYR 0.018 0.001 TYR A 48 PHE 0.013 0.001 PHE B 551 TRP 0.013 0.001 TRP C 49 HIS 0.002 0.001 HIS C 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (18718) covalent geometry : angle 0.57731 / 0.29 (25463) hydrogen bonds : bond 0.04304 / 2.85 ( 911) hydrogen bonds : angle 4.39829 / 3.14 ( 2502) Misc. bond : bond 0.00066 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7597.55 seconds wall clock time: 129 minutes 59.82 seconds (7799.82 seconds total)