Starting phenix.real_space_refine on Sat Dec 28 07:12:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c58_45207/12_2024/9c58_45207.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c58_45207/12_2024/9c58_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_45207/12_2024/9c58_45207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c58_45207/12_2024/9c58_45207.map" model { file = "/net/cci-nas-00/data/ceres_data/9c58_45207/12_2024/9c58_45207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c58_45207/12_2024/9c58_45207.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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, 'TYR:plan': 19, 'ASN:plan1': 20, 'TRP:plan': 4, 'HIS:plan': 16, 'PHE:plan': 15, 'GLU:plan': 33, 'ARG:plan': 24} 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, 'HIS:plan': 9, 'TYR:plan': 18, 'ASN:plan1': 27, 'TRP:plan': 4, 'ASP:plan': 26, 'PHE:plan': 13, 'GLU:plan': 30, 'ARG:plan': 31} 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: {'GLN:plan1': 4, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 11, 'GLU:plan': 11, 'HIS:plan': 5} 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: {'GLN:plan1': 7, 'ASP:plan': 9, 'TYR:plan': 5, 'ASN:plan1': 10, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 14, 'ARG:plan': 4} 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: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 9, 'TRP:plan': 4, 'ASP:plan': 9, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 11} 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: 6.08, per 1000 atoms: 0.76 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: 2.50 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.11 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: 2.73 Time building geometry restraints manager: 2.79 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: 2.090 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.060 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.830 ------------------------------------------------------------------------------- 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= 0.228 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), 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 TRP 0.000 0.000 TRP D 74 PHE 0.000 0.000 PHE D 77 TYR 0.000 0.000 TYR D 35 *********************** 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 : 0.950 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0941 time to fit residues: 8.7871 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 : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 7949 Z= 0.294 Angle : 0.572 5.135 11088 Z= 0.399 Chirality : 0.042 0.148 1542 Planarity : 0.004 0.022 1588 Dihedral : 9.465 171.618 1598 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.21), residues: 1578 helix: 0.29 (0.15), residues: 1021 sheet: -0.22 (0.51), residues: 90 loop : 0.67 (0.33), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP D 74 PHE 0.000 0.000 PHE D 77 TYR 0.000 0.000 TYR D 35 *********************** 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 : 0.826 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0843 time to fit residues: 8.0621 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 : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 142 optimal weight: 40.0000 chunk 49 optimal weight: 3.9990 chunk 115 optimal weight: 20.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.7919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 7949 Z= 0.463 Angle : 0.788 9.318 11088 Z= 0.555 Chirality : 0.044 0.147 1542 Planarity : 0.006 0.025 1588 Dihedral : 10.512 166.773 1598 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.95 % Favored : 89.92 % 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 : 1.82 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.20), residues: 1578 helix: -1.73 (0.14), residues: 994 sheet: -0.53 (0.57), residues: 81 loop : -1.30 (0.30), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP D 74 PHE 0.000 0.000 PHE D 77 TYR 0.000 0.000 TYR D 35 *********************** 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 : 1.016 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0882 time to fit residues: 8.5035 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 : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 40.0000 chunk 108 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 152 optimal weight: 40.0000 chunk 75 optimal weight: 0.0980 chunk 136 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.7429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7949 Z= 0.113 Angle : 0.403 8.256 11088 Z= 0.254 Chirality : 0.040 0.130 1542 Planarity : 0.002 0.016 1588 Dihedral : 8.340 154.424 1598 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1578 helix: 0.25 (0.15), residues: 1059 sheet: -0.41 (0.55), residues: 87 loop : -0.94 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP D 74 PHE 0.000 0.000 PHE D 77 TYR 0.000 0.000 TYR D 35 *********************** 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 : 0.965 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0733 time to fit residues: 7.3629 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 : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 113 optimal weight: 30.0000 chunk 63 optimal weight: 5.9990 chunk 130 optimal weight: 0.5980 chunk 105 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 overall best weight: 5.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.8780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 7949 Z= 0.370 Angle : 0.646 10.105 11088 Z= 0.453 Chirality : 0.042 0.138 1542 Planarity : 0.004 0.022 1588 Dihedral : 9.103 149.113 1598 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.65 % Favored : 89.29 % Rotamer: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.20), residues: 1578 helix: -1.18 (0.15), residues: 1021 sheet: -0.91 (0.62), residues: 72 loop : -1.56 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP D 74 PHE 0.000 0.000 PHE D 77 TYR 0.000 0.000 TYR D 35 *********************** 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 : 0.880 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0730 time to fit residues: 7.3474 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 : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 1.9990 chunk 137 optimal weight: 20.0000 chunk 30 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 152 optimal weight: 50.0000 chunk 126 optimal weight: 7.9990 chunk 70 optimal weight: 0.5980 chunk 12 optimal weight: 0.0870 chunk 50 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.8404 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= 0.098 Angle : 0.389 10.067 11088 Z= 0.240 Chirality : 0.040 0.128 1542 Planarity : 0.002 0.012 1588 Dihedral : 7.606 139.877 1598 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 1.12 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.22), residues: 1578 helix: 0.64 (0.16), residues: 1062 sheet: -0.53 (0.58), residues: 81 loop : -1.36 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP D 74 PHE 0.000 0.000 PHE D 77 TYR 0.000 0.000 TYR D 35 *********************** 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 46 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.865 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0750 time to fit residues: 7.6983 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 : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 152 optimal weight: 20.0000 chunk 95 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.9208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7949 Z= 0.287 Angle : 0.550 10.582 11088 Z= 0.375 Chirality : 0.041 0.139 1542 Planarity : 0.004 0.018 1588 Dihedral : 8.191 137.247 1598 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.21), residues: 1578 helix: -0.56 (0.15), residues: 1048 sheet: 0.16 (0.71), residues: 57 loop : -1.76 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP D 74 PHE 0.000 0.000 PHE D 77 TYR 0.000 0.000 TYR D 35 *********************** 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 44 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.929 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0719 time to fit residues: 7.0648 Evaluate side-chains 44 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 45 optimal weight: 0.0030 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.8990 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= 0.098 Angle : 0.384 10.321 11088 Z= 0.236 Chirality : 0.040 0.128 1542 Planarity : 0.002 0.011 1588 Dihedral : 7.266 136.861 1598 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.22), residues: 1578 helix: 1.07 (0.16), residues: 1062 sheet: -0.63 (0.59), residues: 81 loop : -1.46 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP D 74 PHE 0.000 0.000 PHE D 77 TYR 0.000 0.000 TYR D 35 *********************** 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 45 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.988 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0771 time to fit residues: 7.7769 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 : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 111 optimal weight: 0.0770 chunk 43 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.9412 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= 0.190 Angle : 0.446 9.958 11088 Z= 0.292 Chirality : 0.040 0.132 1542 Planarity : 0.002 0.012 1588 Dihedral : 7.499 132.374 1598 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.22), residues: 1578 helix: 0.59 (0.16), residues: 1057 sheet: -0.18 (0.70), residues: 61 loop : -1.67 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP D 74 PHE 0.000 0.000 PHE D 77 TYR 0.000 0.000 TYR D 35 *********************** 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 45 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.901 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0708 time to fit residues: 7.1510 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 : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 0.6980 chunk 71 optimal weight: 7.9990 chunk 104 optimal weight: 20.0000 chunk 157 optimal weight: 30.0000 chunk 144 optimal weight: 30.0000 chunk 125 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 133 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 1.0154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 7949 Z= 0.216 Angle : 0.490 12.521 11088 Z= 0.321 Chirality : 0.041 0.149 1542 Planarity : 0.003 0.015 1588 Dihedral : 7.652 122.092 1598 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.21), residues: 1578 helix: 0.08 (0.16), residues: 1051 sheet: -0.39 (0.63), residues: 74 loop : -1.92 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP D 74 PHE 0.000 0.000 PHE D 77 TYR 0.000 0.000 TYR D 35 ********************** 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 : 0.941 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0767 time to fit residues: 7.8489 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 : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 34 optimal weight: 0.1980 chunk 125 optimal weight: 3.9990 chunk 52 optimal weight: 30.0000 chunk 128 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.104737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.082621 restraints weight = 40497.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.080584 restraints weight = 56836.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.081125 restraints weight = 56846.250| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 1.0215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 7949 Z= 0.147 Angle : 0.419 11.337 11088 Z= 0.264 Chirality : 0.040 0.134 1542 Planarity : 0.002 0.012 1588 Dihedral : 7.094 116.947 1598 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.22), residues: 1578 helix: 0.76 (0.16), residues: 1056 sheet: 0.40 (0.75), residues: 57 loop : -1.72 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP D 74 PHE 0.000 0.000 PHE D 77 TYR 0.000 0.000 TYR D 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1320.00 seconds wall clock time: 24 minutes 43.26 seconds (1483.26 seconds total)