Starting phenix.real_space_refine on Wed Sep 17 10:16:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c58_45207/09_2025/9c58_45207.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c58_45207/09_2025/9c58_45207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c58_45207/09_2025/9c58_45207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c58_45207/09_2025/9c58_45207.map" model { file = "/net/cci-nas-00/data/ceres_data/9c58_45207/09_2025/9c58_45207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c58_45207/09_2025/9c58_45207.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 C 4739 2.51 5 N 1598 2.21 5 O 1613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7954 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 2900 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 515} Link IDs: {'PTRANS': 20, 'TRANS': 563} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1784 Unresolved non-hydrogen angles: 2271 Unresolved non-hydrogen dihedrals: 1464 Unresolved non-hydrogen chiralities: 190 Planarities with less than four sites: {'GLN:plan1': 33, 'ASP:plan': 28, 'ARG:plan': 24, 'ASN:plan1': 20, 'HIS:plan': 16, 'GLU:plan': 33, 'TYR:plan': 19, 'TRP:plan': 4, 'PHE:plan': 15} Unresolved non-hydrogen planarities: 867 Chain: "B" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 2835 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 509} Link IDs: {'PTRANS': 24, 'TRANS': 545} Chain breaks: 1 Unresolved chain link angles: 24 Unresolved non-hydrogen bonds: 1766 Unresolved non-hydrogen angles: 2241 Unresolved non-hydrogen dihedrals: 1441 Unresolved non-hydrogen chiralities: 191 Planarities with less than four sites: {'GLN:plan1': 28, 'GLU:plan': 30, 'ASN:plan1': 27, 'ASP:plan': 26, 'ARG:plan': 31, 'PHE:plan': 13, 'TYR:plan': 18, 'HIS:plan': 9, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 831 Chain: "M" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 617 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 6, 'TRANS': 117} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 419 Unresolved non-hydrogen angles: 544 Unresolved non-hydrogen dihedrals: 354 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'HIS:plan': 5, 'PHE:plan': 11, 'ASN:plan1': 4, 'ASP:plan': 8, 'GLU:plan': 11, 'TRP:plan': 1, 'GLN:plan1': 4, 'TYR:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 241 Chain: "S" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 747 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 2, 'TRANS': 148} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 493 Unresolved non-hydrogen angles: 630 Unresolved non-hydrogen dihedrals: 401 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'PHE:plan': 9, 'ASN:plan1': 10, 'HIS:plan': 5, 'ARG:plan': 4, 'TYR:plan': 5, 'GLN:plan1': 7, 'GLU:plan': 14, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 275 Chain: "A" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 822 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 3, 'TRANS': 157} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 497 Unresolved non-hydrogen angles: 644 Unresolved non-hydrogen dihedrals: 412 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'ARG:plan': 11, 'TYR:plan': 5, 'GLU:plan': 11, 'PHE:plan': 5, 'ASN:plan1': 9, 'TRP:plan': 4, 'ASP:plan': 9, 'HIS:plan': 3, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 289 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.48, per 1000 atoms: 0.31 Number of scatterers: 7954 At special positions: 0 Unit cell: (97.336, 102.626, 151.294, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) P 3 15.00 Mg 1 11.99 O 1613 8.00 N 1598 7.00 C 4739 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 388.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3066 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 5 sheets defined 75.1% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'D' and resid 18 through 28 Processing helix chain 'D' and resid 31 through 48 removed outlier: 3.798A pdb=" N LYS D 48 " --> pdb=" O LYS D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 69 removed outlier: 3.793A pdb=" N LYS D 55 " --> pdb=" O ASN D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 75 through 84 Processing helix chain 'D' and resid 87 through 102 removed outlier: 4.320A pdb=" N ILE D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 111 Processing helix chain 'D' and resid 112 through 122 Processing helix chain 'D' and resid 124 through 136 removed outlier: 3.550A pdb=" N THR D 128 " --> pdb=" O SER D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 155 removed outlier: 5.245A pdb=" N ASN D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASP D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 177 removed outlier: 3.514A pdb=" N ARG D 163 " --> pdb=" O LYS D 159 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU D 168 " --> pdb=" O LYS D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 192 Proline residue: D 186 - end of helix Processing helix chain 'D' and resid 196 through 212 Processing helix chain 'D' and resid 214 through 220 removed outlier: 3.752A pdb=" N LEU D 219 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N SER D 220 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 232 Processing helix chain 'D' and resid 234 through 249 Processing helix chain 'D' and resid 252 through 270 removed outlier: 3.688A pdb=" N GLY D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLU D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Proline residue: D 262 - end of helix Processing helix chain 'D' and resid 272 through 291 Processing helix chain 'D' and resid 297 through 313 Processing helix chain 'D' and resid 316 through 334 Processing helix chain 'D' and resid 334 through 339 removed outlier: 3.736A pdb=" N VAL D 338 " --> pdb=" O HIS D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 347 Processing helix chain 'D' and resid 348 through 351 Processing helix chain 'D' and resid 353 through 367 Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 389 through 406 Processing helix chain 'D' and resid 414 through 427 Processing helix chain 'D' and resid 433 through 448 Processing helix chain 'D' and resid 451 through 465 Processing helix chain 'D' and resid 465 through 470 Processing helix chain 'D' and resid 477 through 492 removed outlier: 4.061A pdb=" N VAL D 481 " --> pdb=" O GLY D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 496 Processing helix chain 'D' and resid 498 through 507 Processing helix chain 'D' and resid 508 through 514 removed outlier: 3.587A pdb=" N THR D 513 " --> pdb=" O ARG D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 541 removed outlier: 3.559A pdb=" N ALA D 540 " --> pdb=" O GLN D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 554 Processing helix chain 'D' and resid 556 through 562 removed outlier: 4.019A pdb=" N PHE D 560 " --> pdb=" O ARG D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 588 removed outlier: 3.508A pdb=" N LYS D 588 " --> pdb=" O LYS D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 599 removed outlier: 4.539A pdb=" N GLU D 595 " --> pdb=" O PRO D 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 55 through 72 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 79 through 85 Processing helix chain 'B' and resid 91 through 106 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 116 through 124 removed outlier: 3.699A pdb=" N PHE B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 142 Processing helix chain 'B' and resid 147 through 161 Processing helix chain 'B' and resid 163 through 181 Processing helix chain 'B' and resid 184 through 197 removed outlier: 3.726A pdb=" N LYS B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 215 removed outlier: 4.036A pdb=" N SER B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 225 through 233 Processing helix chain 'B' and resid 237 through 256 Processing helix chain 'B' and resid 295 through 305 Processing helix chain 'B' and resid 306 through 310 removed outlier: 3.596A pdb=" N GLN B 309 " --> pdb=" O PRO B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 326 removed outlier: 3.738A pdb=" N HIS B 325 " --> pdb=" O GLN B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 334 Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 346 through 362 removed outlier: 3.871A pdb=" N ILE B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 376 removed outlier: 5.123A pdb=" N LYS B 373 " --> pdb=" O PRO B 370 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 374 " --> pdb=" O TYR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 397 Processing helix chain 'B' and resid 401 through 414 removed outlier: 4.158A pdb=" N LYS B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 435 Processing helix chain 'B' and resid 438 through 450 removed outlier: 3.827A pdb=" N CYS B 448 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 472 removed outlier: 3.665A pdb=" N VAL B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 487 removed outlier: 4.193A pdb=" N HIS B 482 " --> pdb=" O GLU B 478 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 486 " --> pdb=" O HIS B 482 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 487 " --> pdb=" O MET B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 490 No H-bonds generated for 'chain 'B' and resid 488 through 490' Processing helix chain 'B' and resid 492 through 506 removed outlier: 3.707A pdb=" N LEU B 500 " --> pdb=" O ARG B 496 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP B 501 " --> pdb=" O ALA B 497 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 502 " --> pdb=" O SER B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 525 removed outlier: 3.571A pdb=" N VAL B 517 " --> pdb=" O ILE B 513 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS B 523 " --> pdb=" O ARG B 519 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER B 524 " --> pdb=" O LYS B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 528 No H-bonds generated for 'chain 'B' and resid 526 through 528' Processing helix chain 'B' and resid 529 through 564 removed outlier: 3.604A pdb=" N GLN B 535 " --> pdb=" O LEU B 531 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LYS B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLN B 550 " --> pdb=" O THR B 546 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU B 553 " --> pdb=" O LYS B 549 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 582 removed outlier: 3.763A pdb=" N ASP B 572 " --> pdb=" O TYR B 568 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG B 573 " --> pdb=" O ASP B 569 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG B 578 " --> pdb=" O THR B 574 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 587 removed outlier: 3.619A pdb=" N LYS B 586 " --> pdb=" O PRO B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 593 Processing helix chain 'B' and resid 593 through 600 Processing helix chain 'B' and resid 611 through 617 removed outlier: 4.035A pdb=" N HIS B 616 " --> pdb=" O ASP B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 627 Processing helix chain 'B' and resid 645 through 650 removed outlier: 3.638A pdb=" N VAL B 648 " --> pdb=" O ASP B 645 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 27 No H-bonds generated for 'chain 'M' and resid 25 through 27' Processing helix chain 'M' and resid 28 through 39 removed outlier: 4.234A pdb=" N PHE M 32 " --> pdb=" O VAL M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 95 removed outlier: 3.613A pdb=" N VAL M 79 " --> pdb=" O PRO M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 105 removed outlier: 3.556A pdb=" N ILE M 102 " --> pdb=" O SER M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 116 Processing helix chain 'S' and resid 24 through 41 removed outlier: 4.188A pdb=" N LYS S 41 " --> pdb=" O HIS S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 57 removed outlier: 3.779A pdb=" N ILE S 56 " --> pdb=" O GLY S 53 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY S 57 " --> pdb=" O LEU S 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 57' Processing helix chain 'S' and resid 82 through 101 Processing helix chain 'S' and resid 105 through 112 removed outlier: 3.560A pdb=" N LEU S 109 " --> pdb=" O CYS S 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 112 through 123 Processing helix chain 'S' and resid 133 through 151 Processing helix chain 'A' and resid 29 through 40 Processing helix chain 'A' and resid 71 through 82 Proline residue: A 76 - end of helix removed outlier: 3.535A pdb=" N ARG A 79 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 135 through 144 Processing helix chain 'A' and resid 145 through 148 Processing helix chain 'A' and resid 165 through 178 Processing sheet with id=AA1, first strand: chain 'M' and resid 14 through 19 removed outlier: 4.096A pdb=" N SER M 4 " --> pdb=" O VAL M 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 117 through 118 Processing sheet with id=AA3, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.473A pdb=" N ILE S 7 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER S 17 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE S 5 " --> pdb=" O SER S 17 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N PHE S 19 " --> pdb=" O LYS S 3 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N LYS S 3 " --> pdb=" O PHE S 19 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 124 through 125 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 58 removed outlier: 6.607A pdb=" N ARG A 19 " --> pdb=" O GLY A 87 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE A 89 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU A 21 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL A 91 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A 23 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ASP A 93 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU A 88 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N PHE A 124 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE A 90 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASN A 126 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL A 92 " --> pdb=" O ASN A 126 " (cutoff:3.500A) 810 hydrogen bonds defined for protein. 2319 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.30: 1596 1.30 - 1.38: 1594 1.38 - 1.46: 1292 1.46 - 1.54: 3411 1.54 - 1.63: 56 Bond restraints: 7949 Sorted by residual: bond pdb=" CA VAL A 53 " pdb=" CB VAL A 53 " ideal model delta sigma weight residual 1.544 1.573 -0.029 1.46e-02 4.69e+03 4.01e+00 bond pdb=" CA VAL A 100 " pdb=" C VAL A 100 " ideal model delta sigma weight residual 1.523 1.551 -0.028 1.46e-02 4.69e+03 3.70e+00 bond pdb=" O1A GTP A1001 " pdb=" PA GTP A1001 " ideal model delta sigma weight residual 1.510 1.472 0.038 2.00e-02 2.50e+03 3.55e+00 bond pdb=" O1B GTP A1001 " pdb=" PB GTP A1001 " ideal model delta sigma weight residual 1.510 1.474 0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" CA VAL A 56 " pdb=" CB VAL A 56 " ideal model delta sigma weight residual 1.539 1.559 -0.020 1.18e-02 7.18e+03 2.82e+00 ... (remaining 7944 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 10854 1.98 - 3.96: 205 3.96 - 5.94: 24 5.94 - 7.92: 3 7.92 - 9.90: 2 Bond angle restraints: 11088 Sorted by residual: angle pdb=" N MET D 170 " pdb=" CA MET D 170 " pdb=" CB MET D 170 " ideal model delta sigma weight residual 110.28 115.94 -5.66 1.55e+00 4.16e-01 1.34e+01 angle pdb=" C LEU B 51 " pdb=" N GLU B 52 " pdb=" CA GLU B 52 " ideal model delta sigma weight residual 122.38 116.04 6.34 1.81e+00 3.05e-01 1.23e+01 angle pdb=" N GLU S 122 " pdb=" CA GLU S 122 " pdb=" CB GLU S 122 " ideal model delta sigma weight residual 110.28 115.69 -5.41 1.55e+00 4.16e-01 1.22e+01 angle pdb=" C ALA S 121 " pdb=" N GLU S 122 " pdb=" CA GLU S 122 " ideal model delta sigma weight residual 120.31 115.01 5.30 1.52e+00 4.33e-01 1.22e+01 angle pdb=" C1' GTP A1001 " pdb=" C2' GTP A1001 " pdb=" C3' GTP A1001 " ideal model delta sigma weight residual 111.00 101.10 9.90 3.00e+00 1.11e-01 1.09e+01 ... (remaining 11083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 4672 35.80 - 71.59: 6 71.59 - 107.39: 2 107.39 - 143.18: 2 143.18 - 178.98: 2 Dihedral angle restraints: 4684 sinusoidal: 34 harmonic: 4650 Sorted by residual: dihedral pdb=" O3B GTP A1001 " pdb=" O3A GTP A1001 " pdb=" PB GTP A1001 " pdb=" PA GTP A1001 " ideal model delta sinusoidal sigma weight residual -68.92 110.06 -178.98 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP A1001 " pdb=" C1' GTP A1001 " pdb=" N9 GTP A1001 " pdb=" O4' GTP A1001 " ideal model delta sinusoidal sigma weight residual 104.59 -70.84 175.44 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' GTP A1001 " pdb=" O5' GTP A1001 " pdb=" PA GTP A1001 " pdb=" O3A GTP A1001 " ideal model delta sinusoidal sigma weight residual 69.27 -60.74 130.01 1 2.00e+01 2.50e-03 3.94e+01 ... (remaining 4681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1178 0.055 - 0.110: 304 0.110 - 0.166: 41 0.166 - 0.221: 13 0.221 - 0.276: 6 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CA ASN A 135 " pdb=" N ASN A 135 " pdb=" C ASN A 135 " pdb=" CB ASN A 135 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA TYR A 167 " pdb=" N TYR A 167 " pdb=" C TYR A 167 " pdb=" CB TYR A 167 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA TYR A 35 " pdb=" N TYR A 35 " pdb=" C TYR A 35 " pdb=" CB TYR A 35 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1539 not shown) Planarity restraints: 1588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 107 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C GLU B 107 " -0.024 2.00e-02 2.50e+03 pdb=" O GLU B 107 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU B 108 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 581 " -0.006 2.00e-02 2.50e+03 1.27e-02 1.62e+00 pdb=" C HIS D 581 " 0.022 2.00e-02 2.50e+03 pdb=" O HIS D 581 " -0.008 2.00e-02 2.50e+03 pdb=" N ILE D 582 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 167 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.27e+00 pdb=" C VAL D 167 " 0.020 2.00e-02 2.50e+03 pdb=" O VAL D 167 " -0.007 2.00e-02 2.50e+03 pdb=" N LEU D 168 " -0.007 2.00e-02 2.50e+03 ... (remaining 1585 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 5 2.40 - 3.03: 5192 3.03 - 3.65: 12473 3.65 - 4.28: 14145 4.28 - 4.90: 22210 Nonbonded interactions: 54025 Sorted by model distance: nonbonded pdb=" CB ASN D 114 " pdb=" O PHE A 51 " model vdw 1.776 3.440 nonbonded pdb="MG MG A1000 " pdb=" O2G GTP A1001 " model vdw 1.940 2.170 nonbonded pdb=" OG1 THR A 48 " pdb="MG MG A1000 " model vdw 2.068 2.170 nonbonded pdb=" OG1 THR A 31 " pdb="MG MG A1000 " model vdw 2.168 2.170 nonbonded pdb="MG MG A1000 " pdb=" O2B GTP A1001 " model vdw 2.205 2.170 ... (remaining 54020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.970 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 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 : 0.003 0.038 7949 Z= 0.227 Angle : 0.727 9.904 11088 Z= 0.483 Chirality : 0.052 0.276 1542 Planarity : 0.002 0.014 1588 Dihedral : 10.281 178.979 1618 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.21), residues: 1578 helix: 0.48 (0.16), residues: 1020 sheet: -0.00 (0.48), residues: 93 loop : 0.78 (0.33), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR D 35 PHE 0.000 0.000 PHE D 77 TRP 0.000 0.000 TRP D 74 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 7949) covalent geometry : angle 0.72655 (11088) hydrogen bonds : bond 0.19003 ( 810) hydrogen bonds : angle 6.99749 ( 2319) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.284 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0414 time to fit residues: 3.7079 Evaluate side-chains 45 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 0.1980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 30.0000 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.118215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.092224 restraints weight = 39251.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.092395 restraints weight = 38509.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.092396 restraints weight = 37687.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.092396 restraints weight = 37609.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.092396 restraints weight = 37609.245| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7949 Z= 0.183 Angle : 0.439 6.101 11088 Z= 0.291 Chirality : 0.040 0.145 1542 Planarity : 0.003 0.020 1588 Dihedral : 8.942 172.499 1598 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.21), residues: 1578 helix: 1.64 (0.16), residues: 1033 sheet: 0.27 (0.52), residues: 89 loop : 1.22 (0.33), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR D 35 PHE 0.000 0.000 PHE D 77 TRP 0.000 0.000 TRP D 74 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 7949) covalent geometry : angle 0.43937 (11088) hydrogen bonds : bond 0.04066 ( 810) hydrogen bonds : angle 4.66554 ( 2319) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.258 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0338 time to fit residues: 3.2171 Evaluate side-chains 45 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 14 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 79 optimal weight: 0.0870 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 150 optimal weight: 0.9990 chunk 156 optimal weight: 30.0000 chunk 8 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.118514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.095244 restraints weight = 38428.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.093873 restraints weight = 43371.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.093813 restraints weight = 43424.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.093719 restraints weight = 45246.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.093709 restraints weight = 43534.180| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 7949 Z= 0.087 Angle : 0.344 5.413 11088 Z= 0.215 Chirality : 0.039 0.128 1542 Planarity : 0.002 0.015 1588 Dihedral : 7.737 156.185 1598 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.24 (0.22), residues: 1578 helix: 2.65 (0.16), residues: 1046 sheet: 0.41 (0.51), residues: 83 loop : 1.41 (0.34), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR D 35 PHE 0.000 0.000 PHE D 77 TRP 0.000 0.000 TRP D 74 Details of bonding type rmsd covalent geometry : bond 0.00117 ( 7949) covalent geometry : angle 0.34376 (11088) hydrogen bonds : bond 0.02723 ( 810) hydrogen bonds : angle 3.71723 ( 2319) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.386 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0406 time to fit residues: 3.8973 Evaluate side-chains 45 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 97 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 39 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.104409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.080746 restraints weight = 42552.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.080680 restraints weight = 43514.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.080680 restraints weight = 43839.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.080680 restraints weight = 43839.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.080680 restraints weight = 43839.439| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.6487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 7949 Z= 0.388 Angle : 0.648 7.080 11088 Z= 0.456 Chirality : 0.042 0.135 1542 Planarity : 0.005 0.024 1588 Dihedral : 9.212 157.675 1598 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.21), residues: 1578 helix: -0.21 (0.15), residues: 1021 sheet: -0.25 (0.55), residues: 86 loop : -0.42 (0.31), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR D 35 PHE 0.000 0.000 PHE D 77 TRP 0.000 0.000 TRP D 74 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 7949) covalent geometry : angle 0.64836 (11088) hydrogen bonds : bond 0.06558 ( 810) hydrogen bonds : angle 6.64427 ( 2319) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.326 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0363 time to fit residues: 3.4642 Evaluate side-chains 45 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 43 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 144 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 1 optimal weight: 3.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.107561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.083481 restraints weight = 41203.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.083463 restraints weight = 41265.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.083463 restraints weight = 41303.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.083463 restraints weight = 41303.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.083463 restraints weight = 41303.612| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.6630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 7949 Z= 0.178 Angle : 0.434 6.020 11088 Z= 0.287 Chirality : 0.040 0.134 1542 Planarity : 0.002 0.015 1588 Dihedral : 7.976 149.792 1598 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.21), residues: 1578 helix: 0.63 (0.16), residues: 1041 sheet: -0.11 (0.56), residues: 82 loop : -0.31 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR D 35 PHE 0.000 0.000 PHE D 77 TRP 0.000 0.000 TRP D 74 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 7949) covalent geometry : angle 0.43384 (11088) hydrogen bonds : bond 0.03916 ( 810) hydrogen bonds : angle 5.01006 ( 2319) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.301 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0367 time to fit residues: 3.5327 Evaluate side-chains 45 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.104335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.083539 restraints weight = 42056.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.081569 restraints weight = 68082.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.081685 restraints weight = 73128.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.081574 restraints weight = 67742.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.081720 restraints weight = 60825.745| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.8131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 7949 Z= 0.242 Angle : 0.510 8.225 11088 Z= 0.345 Chirality : 0.041 0.139 1542 Planarity : 0.003 0.018 1588 Dihedral : 8.000 140.728 1598 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.21), residues: 1578 helix: 0.06 (0.15), residues: 1049 sheet: -0.24 (0.58), residues: 79 loop : -0.85 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR D 35 PHE 0.000 0.000 PHE D 77 TRP 0.000 0.000 TRP D 74 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7949) covalent geometry : angle 0.50968 (11088) hydrogen bonds : bond 0.04825 ( 810) hydrogen bonds : angle 5.71008 ( 2319) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.304 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0366 time to fit residues: 3.4554 Evaluate side-chains 45 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 52 optimal weight: 30.0000 chunk 10 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.108346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.085747 restraints weight = 40671.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.084722 restraints weight = 38586.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.084486 restraints weight = 39155.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.084499 restraints weight = 39501.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.084397 restraints weight = 41163.784| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.8043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 7949 Z= 0.107 Angle : 0.373 6.852 11088 Z= 0.233 Chirality : 0.040 0.140 1542 Planarity : 0.002 0.011 1588 Dihedral : 6.966 130.819 1598 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.22), residues: 1578 helix: 1.31 (0.16), residues: 1057 sheet: -0.23 (0.57), residues: 81 loop : -0.57 (0.33), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR D 35 PHE 0.000 0.000 PHE D 77 TRP 0.000 0.000 TRP D 74 Details of bonding type rmsd covalent geometry : bond 0.00142 ( 7949) covalent geometry : angle 0.37267 (11088) hydrogen bonds : bond 0.03002 ( 810) hydrogen bonds : angle 4.34268 ( 2319) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.342 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0364 time to fit residues: 3.5760 Evaluate side-chains 46 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 140 optimal weight: 20.0000 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.109028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.087132 restraints weight = 40372.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.085820 restraints weight = 50133.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.085966 restraints weight = 52454.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.085921 restraints weight = 48788.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.085912 restraints weight = 47719.173| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.8258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.011 7949 Z= 0.108 Angle : 0.366 5.426 11088 Z= 0.227 Chirality : 0.040 0.128 1542 Planarity : 0.002 0.011 1588 Dihedral : 6.327 115.183 1598 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.22), residues: 1578 helix: 2.07 (0.16), residues: 1058 sheet: -0.14 (0.57), residues: 81 loop : -0.50 (0.33), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR D 35 PHE 0.000 0.000 PHE D 77 TRP 0.000 0.000 TRP D 74 Details of bonding type rmsd covalent geometry : bond 0.00143 ( 7949) covalent geometry : angle 0.36554 (11088) hydrogen bonds : bond 0.02754 ( 810) hydrogen bonds : angle 3.99033 ( 2319) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.324 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0360 time to fit residues: 3.5052 Evaluate side-chains 46 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 116 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 124 optimal weight: 30.0000 chunk 27 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.103284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.082288 restraints weight = 41503.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.080334 restraints weight = 63053.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.080616 restraints weight = 69534.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.080679 restraints weight = 59294.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.080782 restraints weight = 56309.674| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.9123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 7949 Z= 0.267 Angle : 0.519 7.152 11088 Z= 0.351 Chirality : 0.041 0.134 1542 Planarity : 0.003 0.015 1588 Dihedral : 7.040 102.818 1598 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.21), residues: 1578 helix: 0.37 (0.15), residues: 1054 sheet: -0.33 (0.60), residues: 79 loop : -1.30 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR D 35 PHE 0.000 0.000 PHE D 77 TRP 0.000 0.000 TRP D 74 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 7949) covalent geometry : angle 0.51887 (11088) hydrogen bonds : bond 0.04842 ( 810) hydrogen bonds : angle 5.62056 ( 2319) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.309 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0370 time to fit residues: 3.6180 Evaluate side-chains 46 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 111 optimal weight: 7.9990 chunk 122 optimal weight: 0.0270 chunk 117 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 156 optimal weight: 30.0000 chunk 30 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.105325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.083597 restraints weight = 40779.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.081650 restraints weight = 57963.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.082037 restraints weight = 58560.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.081821 restraints weight = 55349.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.081797 restraints weight = 52160.580| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.9296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 7949 Z= 0.171 Angle : 0.437 8.224 11088 Z= 0.278 Chirality : 0.040 0.132 1542 Planarity : 0.002 0.013 1588 Dihedral : 6.252 87.352 1598 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.22), residues: 1578 helix: 0.80 (0.16), residues: 1058 sheet: -0.37 (0.58), residues: 80 loop : -1.26 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR D 35 PHE 0.000 0.000 PHE D 77 TRP 0.000 0.000 TRP D 74 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 7949) covalent geometry : angle 0.43712 (11088) hydrogen bonds : bond 0.03567 ( 810) hydrogen bonds : angle 4.78417 ( 2319) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.300 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0357 time to fit residues: 3.4628 Evaluate side-chains 46 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 140 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 20.0000 chunk 79 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 128 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.108329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.086772 restraints weight = 40093.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.084693 restraints weight = 59779.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.085175 restraints weight = 62266.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.085187 restraints weight = 53960.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.085189 restraints weight = 51416.365| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.9289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.011 7949 Z= 0.095 Angle : 0.374 7.351 11088 Z= 0.223 Chirality : 0.040 0.129 1542 Planarity : 0.002 0.011 1588 Dihedral : 5.446 81.575 1598 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.22), residues: 1578 helix: 1.92 (0.16), residues: 1062 sheet: -0.32 (0.58), residues: 80 loop : -1.12 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR D 35 PHE 0.000 0.000 PHE D 77 TRP 0.000 0.000 TRP D 74 Details of bonding type rmsd covalent geometry : bond 0.00126 ( 7949) covalent geometry : angle 0.37415 (11088) hydrogen bonds : bond 0.02675 ( 810) hydrogen bonds : angle 4.03406 ( 2319) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1328.87 seconds wall clock time: 23 minutes 21.25 seconds (1401.25 seconds total)