Starting phenix.real_space_refine on Fri Sep 11 19:36:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zji_11234/09_2026/6zji_11234.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zji_11234/09_2026/6zji_11234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zji_11234/09_2026/6zji_11234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zji_11234/09_2026/6zji_11234.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6zji_11234/09_2026/6zji_11234.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zji_11234/09_2026/6zji_11234.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zji_11234/09_2026/6zji_11234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zji_11234/09_2026/6zji_11234.map" } resolution = 3.7 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= 0.001 sd= 0.010 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 Fe 2 7.16 5 S 36 5.16 5 C 6893 2.51 5 N 1837 2.21 5 O 2023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10791 Number of models: 1 Model: "" Number of chains: 4 Chain: "AP1" Number of atoms: 5342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 697, 5324 Classifications: {'peptide': 697} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 44, 'TRANS': 652} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Conformer: "B" Number of residues, atoms: 697, 5324 Classifications: {'peptide': 697} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 44, 'TRANS': 652} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 5447 Chain: "BP1" Number of atoms: 5363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5363 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 45, 'TRANS': 654} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "AP1" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "BP1" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.95, per 1000 atoms: 0.27 Number of scatterers: 10791 At special positions: 0 Unit cell: (103.04, 115.2, 81.28, 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) Fe 2 26.01 S 36 16.00 O 2023 8.00 N 1837 7.00 C 6893 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 629.5 milliseconds 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2506 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 7 sheets defined 50.2% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'AP1' and resid 44 through 48 removed outlier: 3.792A pdb=" N VALAP1 47 " --> pdb=" O ASNAP1 44 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 63 through 68 removed outlier: 3.643A pdb=" N VALAP1 68 " --> pdb=" O TYRAP1 64 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 69 through 71 No H-bonds generated for 'chain 'AP1' and resid 69 through 71' Processing helix chain 'AP1' and resid 72 through 86 removed outlier: 3.701A pdb=" N ARGAP1 78 " --> pdb=" O ASPAP1 74 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLUAP1 82 " --> pdb=" O ARGAP1 78 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THRAP1 85 " --> pdb=" O GLUAP1 81 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 93 through 97 Processing helix chain 'AP1' and resid 98 through 111 Processing helix chain 'AP1' and resid 121 through 125 removed outlier: 4.011A pdb=" N GLYAP1 124 " --> pdb=" O GLYAP1 121 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 130 through 135 removed outlier: 3.688A pdb=" N ASNAP1 133 " --> pdb=" O ALAAP1 130 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRPAP1 135 " --> pdb=" O LEUAP1 132 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 140 through 148 removed outlier: 3.705A pdb=" N ALAAP1 144 " --> pdb=" O SERAP1 140 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARGAP1 146 " --> pdb=" O ASPAP1 142 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 148 through 156 removed outlier: 4.385A pdb=" N LYSAP1 154 " --> pdb=" O PROAP1 150 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYRAP1 155 " --> pdb=" O VALAP1 151 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 157 through 159 No H-bonds generated for 'chain 'AP1' and resid 157 through 159' Processing helix chain 'AP1' and resid 160 through 175 removed outlier: 3.540A pdb=" N LEUAP1 173 " --> pdb=" O GLYAP1 169 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLUAP1 174 " --> pdb=" O ASNAP1 170 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 234 through 238 Processing helix chain 'AP1' and resid 240 through 253 removed outlier: 3.639A pdb=" N GLUAP1 250 " --> pdb=" O VALAP1 246 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 254 through 256 No H-bonds generated for 'chain 'AP1' and resid 254 through 256' Processing helix chain 'AP1' and resid 259 through 270 removed outlier: 4.076A pdb=" N ALAAP1 263 " --> pdb=" O ASPAP1 259 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALAAP1 264 " --> pdb=" O VALAP1 260 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEUAP1 265 " --> pdb=" O GLUAP1 261 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 287 through 291 Processing helix chain 'AP1' and resid 292 through 296 Processing helix chain 'AP1' and resid 308 through 312 Processing helix chain 'AP1' and resid 331 through 339 removed outlier: 4.026A pdb=" N TYRAP1 339 " --> pdb=" O ILEAP1 335 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 382 through 387 Processing helix chain 'AP1' and resid 387 through 397 removed outlier: 4.116A pdb=" N ARGAP1 392 " --> pdb=" O PROAP1 388 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILEAP1 393 " --> pdb=" O ILEAP1 389 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 401 through 417 Processing helix chain 'AP1' and resid 422 through 426 removed outlier: 3.698A pdb=" N TYRAP1 426 " --> pdb=" O VALAP1 423 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 454 through 465 removed outlier: 4.102A pdb=" N ARGAP1 463 " --> pdb=" O LYSAP1 459 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 468 through 480 removed outlier: 4.428A pdb=" N SERAP1 474 " --> pdb=" O SERAP1 470 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 492 through 498 removed outlier: 4.408A pdb=" N ARGAP1 496 " --> pdb=" O ASNAP1 493 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILEAP1 497 " --> pdb=" O GLYAP1 494 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARGAP1 498 " --> pdb=" O GLYAP1 495 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 499 through 504 Processing helix chain 'AP1' and resid 513 through 530 removed outlier: 4.015A pdb=" N SERAP1 530 " --> pdb=" O GLUAP1 526 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 540 through 558 Processing helix chain 'AP1' and resid 592 through 596 Processing helix chain 'AP1' and resid 605 through 610 removed outlier: 3.515A pdb=" N METAP1 609 " --> pdb=" O PROAP1 605 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 610 through 617 removed outlier: 3.634A pdb=" N LEUAP1 616 " --> pdb=" O ASPAP1 612 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 620 through 634 Processing helix chain 'AP1' and resid 655 through 663 removed outlier: 3.786A pdb=" N ASPAP1 663 " --> pdb=" O VALAP1 659 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 693 through 701 removed outlier: 3.564A pdb=" N VALAP1 697 " --> pdb=" O ARGAP1 693 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N PHEAP1 698 " --> pdb=" O VALAP1 694 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLYAP1 699 " --> pdb=" O ASPAP1 695 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 701 through 712 removed outlier: 3.532A pdb=" N ALAAP1 706 " --> pdb=" O SERAP1 702 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEUAP1 707 " --> pdb=" O GLUAP1 703 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 716 through 732 Processing helix chain 'BP1' and resid 63 through 68 removed outlier: 3.601A pdb=" N GLUBP1 67 " --> pdb=" O ASPBP1 63 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 69 through 71 No H-bonds generated for 'chain 'BP1' and resid 69 through 71' Processing helix chain 'BP1' and resid 72 through 84 removed outlier: 3.605A pdb=" N GLUBP1 81 " --> pdb=" O THRBP1 77 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLUBP1 82 " --> pdb=" O ARGBP1 78 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 93 through 97 Processing helix chain 'BP1' and resid 98 through 108 Processing helix chain 'BP1' and resid 131 through 135 removed outlier: 3.657A pdb=" N SERBP1 134 " --> pdb=" O PROBP1 131 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 141 through 148 removed outlier: 3.795A pdb=" N LEUBP1 148 " --> pdb=" O ALABP1 144 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 148 through 156 Processing helix chain 'BP1' and resid 160 through 176 Processing helix chain 'BP1' and resid 234 through 238 Processing helix chain 'BP1' and resid 240 through 253 Processing helix chain 'BP1' and resid 254 through 256 No H-bonds generated for 'chain 'BP1' and resid 254 through 256' Processing helix chain 'BP1' and resid 258 through 271 removed outlier: 3.624A pdb=" N THRBP1 262 " --> pdb=" O ASNBP1 258 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALABP1 263 " --> pdb=" O ASPBP1 259 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 280 through 284 removed outlier: 3.848A pdb=" N VALBP1 284 " --> pdb=" O ALABP1 281 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 292 through 296 Processing helix chain 'BP1' and resid 308 through 312 removed outlier: 3.652A pdb=" N ASPBP1 311 " --> pdb=" O THRBP1 308 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 331 through 337 Processing helix chain 'BP1' and resid 357 through 359 No H-bonds generated for 'chain 'BP1' and resid 357 through 359' Processing helix chain 'BP1' and resid 379 through 381 No H-bonds generated for 'chain 'BP1' and resid 379 through 381' Processing helix chain 'BP1' and resid 382 through 387 removed outlier: 3.521A pdb=" N VALBP1 386 " --> pdb=" O LEUBP1 382 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 387 through 395 removed outlier: 3.813A pdb=" N ILEBP1 393 " --> pdb=" O ILEBP1 389 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 396 through 398 No H-bonds generated for 'chain 'BP1' and resid 396 through 398' Processing helix chain 'BP1' and resid 402 through 417 removed outlier: 3.633A pdb=" N ASPBP1 406 " --> pdb=" O GLUBP1 402 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 422 through 426 removed outlier: 3.605A pdb=" N ARGBP1 425 " --> pdb=" O PROBP1 422 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 451 through 466 removed outlier: 4.091A pdb=" N SERBP1 465 " --> pdb=" O GLNBP1 461 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 468 through 479 removed outlier: 3.757A pdb=" N SERBP1 474 " --> pdb=" O SERBP1 470 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALABP1 476 " --> pdb=" O LEUBP1 472 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 492 through 498 removed outlier: 4.316A pdb=" N ARGBP1 496 " --> pdb=" O ASNBP1 493 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILEBP1 497 " --> pdb=" O GLYBP1 494 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 499 through 504 removed outlier: 3.591A pdb=" N GLYBP1 504 " --> pdb=" O GLNBP1 500 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 513 through 531 Processing helix chain 'BP1' and resid 539 through 560 removed outlier: 3.783A pdb=" N LEUBP1 543 " --> pdb=" O SERBP1 539 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 575 through 579 Processing helix chain 'BP1' and resid 582 through 587 removed outlier: 4.120A pdb=" N VALBP1 586 " --> pdb=" O SERBP1 583 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 593 through 596 Processing helix chain 'BP1' and resid 607 through 617 removed outlier: 3.971A pdb=" N LEUBP1 611 " --> pdb=" O GLUBP1 607 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEUBP1 617 " --> pdb=" O LYSBP1 613 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 620 through 634 removed outlier: 3.667A pdb=" N THRBP1 625 " --> pdb=" O ALABP1 621 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEUBP1 627 " --> pdb=" O GLUBP1 623 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 637 through 641 removed outlier: 3.619A pdb=" N LEUBP1 641 " --> pdb=" O TYRBP1 638 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 655 through 662 removed outlier: 3.510A pdb=" N ASNBP1 660 " --> pdb=" O ASPBP1 656 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 692 through 697 removed outlier: 3.997A pdb=" N VALBP1 697 " --> pdb=" O ARGBP1 693 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 698 through 700 No H-bonds generated for 'chain 'BP1' and resid 698 through 700' Processing helix chain 'BP1' and resid 703 through 712 removed outlier: 4.083A pdb=" N LEUBP1 707 " --> pdb=" O GLUBP1 703 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VALBP1 708 " --> pdb=" O LEUBP1 704 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYRBP1 711 " --> pdb=" O LEUBP1 707 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 716 through 732 removed outlier: 4.339A pdb=" N GLNBP1 722 " --> pdb=" O PROBP1 718 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VALBP1 725 " --> pdb=" O VALBP1 721 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALABP1 726 " --> pdb=" O GLNBP1 722 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'AP1' and resid 274 through 275 removed outlier: 3.892A pdb=" N VALAP1 319 " --> pdb=" O THRAP1 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AP1' and resid 341 through 345 removed outlier: 3.563A pdb=" N GLUAP1 342 " --> pdb=" O THRAP1 354 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N METAP1 377 " --> pdb=" O TYRAP1 353 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AP1' and resid 483 through 484 removed outlier: 3.994A pdb=" N ARGAP1 484 " --> pdb=" O ARGAP1 489 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARGAP1 489 " --> pdb=" O ARGAP1 484 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'AP1' and resid 677 through 681 removed outlier: 3.518A pdb=" N TRPAP1 689 " --> pdb=" O GLYAP1 680 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'BP1' and resid 341 through 345 removed outlier: 3.565A pdb=" N METBP1 377 " --> pdb=" O TYRBP1 353 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'BP1' and resid 591 through 592 Processing sheet with id=AA7, first strand: chain 'BP1' and resid 667 through 670 removed outlier: 3.788A pdb=" N GLUBP1 669 " --> pdb=" O GLNBP1 679 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRPBP1 689 " --> pdb=" O GLYBP1 680 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 987 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: 1.68 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 4505 1.39 - 1.55: 6514 1.55 - 1.72: 0 1.72 - 1.88: 70 1.88 - 2.05: 8 Bond restraints: 11097 Sorted by residual: bond pdb=" CA THRBP1 690 " pdb=" C THRBP1 690 " ideal model delta sigma weight residual 1.530 1.517 0.013 1.08e-02 8.57e+03 1.47e+00 bond pdb=" CA LYSBP1 310 " pdb=" C LYSBP1 310 " ideal model delta sigma weight residual 1.522 1.506 0.016 1.41e-02 5.03e+03 1.33e+00 bond pdb=" NA HEMBP1 801 " pdb="FE HEMBP1 801 " ideal model delta sigma weight residual 2.080 2.001 0.079 7.00e-02 2.04e+02 1.26e+00 bond pdb=" CA GLYAP1 156 " pdb=" C GLYAP1 156 " ideal model delta sigma weight residual 1.514 1.530 -0.015 1.41e-02 5.03e+03 1.17e+00 bond pdb=" C LEUBP1 148 " pdb=" N TRPBP1 149 " ideal model delta sigma weight residual 1.332 1.318 0.014 1.33e-02 5.65e+03 1.16e+00 ... (remaining 11092 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 15054 3.02 - 6.03: 98 6.03 - 9.05: 2 9.05 - 12.07: 0 12.07 - 15.08: 2 Bond angle restraints: 15156 Sorted by residual: angle pdb=" CA LEUAP1 430 " pdb=" C LEUAP1 430 " pdb=" N VALAP1 431 " ideal model delta sigma weight residual 116.84 123.25 -6.41 1.71e+00 3.42e-01 1.40e+01 angle pdb=" N ARGAP1 463 " pdb=" CA ARGAP1 463 " pdb=" C ARGAP1 463 " ideal model delta sigma weight residual 114.31 109.88 4.43 1.29e+00 6.01e-01 1.18e+01 angle pdb=" N ILEAP1 462 " pdb=" CA ILEAP1 462 " pdb=" C ILEAP1 462 " ideal model delta sigma weight residual 113.07 109.17 3.90 1.36e+00 5.41e-01 8.24e+00 angle pdb=" CA LEUAP1 430 " pdb=" C LEUAP1 430 " pdb=" O LEUAP1 430 " ideal model delta sigma weight residual 120.51 116.66 3.85 1.43e+00 4.89e-01 7.23e+00 angle pdb=" C GLNAP1 434 " pdb=" N THRAP1 435 " pdb=" CA THRAP1 435 " ideal model delta sigma weight residual 121.54 126.60 -5.06 1.91e+00 2.74e-01 7.02e+00 ... (remaining 15151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 5866 17.81 - 35.62: 479 35.62 - 53.43: 73 53.43 - 71.23: 9 71.23 - 89.04: 11 Dihedral angle restraints: 6438 sinusoidal: 2495 harmonic: 3943 Sorted by residual: dihedral pdb=" CA ALABP1 130 " pdb=" C ALABP1 130 " pdb=" N PROBP1 131 " pdb=" CA PROBP1 131 " ideal model delta harmonic sigma weight residual 180.00 152.41 27.59 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA ALAAP1 130 " pdb=" C ALAAP1 130 " pdb=" N PROAP1 131 " pdb=" CA PROAP1 131 " ideal model delta harmonic sigma weight residual 180.00 160.36 19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA PROAP1 292 " pdb=" C PROAP1 292 " pdb=" N LEUAP1 293 " pdb=" CA LEUAP1 293 " ideal model delta harmonic sigma weight residual 180.00 -162.41 -17.59 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 6435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 787 0.027 - 0.054: 505 0.054 - 0.080: 207 0.080 - 0.107: 80 0.107 - 0.134: 18 Chirality restraints: 1597 Sorted by residual: chirality pdb=" CA PROAP1 288 " pdb=" N PROAP1 288 " pdb=" C PROAP1 288 " pdb=" CB PROAP1 288 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CB THRAP1 324 " pdb=" CA THRAP1 324 " pdb=" OG1 THRAP1 324 " pdb=" CG2 THRAP1 324 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILEAP1 364 " pdb=" N ILEAP1 364 " pdb=" C ILEAP1 364 " pdb=" CB ILEAP1 364 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 1594 not shown) Planarity restraints: 1982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRPBP1 149 " -0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PROBP1 150 " 0.082 5.00e-02 4.00e+02 pdb=" CA PROBP1 150 " -0.024 5.00e-02 4.00e+02 pdb=" CD PROBP1 150 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRPAP1 135 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PROAP1 136 " -0.069 5.00e-02 4.00e+02 pdb=" CA PROAP1 136 " 0.020 5.00e-02 4.00e+02 pdb=" CD PROAP1 136 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALAAP1 130 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PROAP1 131 " -0.068 5.00e-02 4.00e+02 pdb=" CA PROAP1 131 " 0.020 5.00e-02 4.00e+02 pdb=" CD PROAP1 131 " 0.022 5.00e-02 4.00e+02 ... (remaining 1979 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2951 2.79 - 3.32: 10669 3.32 - 3.84: 17646 3.84 - 4.37: 20360 4.37 - 4.90: 33935 Nonbonded interactions: 85561 Sorted by model distance: nonbonded pdb=" OD2 ASPBP1 79 " pdb=" NZ LYSBP1 154 " model vdw 2.261 3.120 nonbonded pdb=" O ARGAP1 128 " pdb=" ND2 ASNAP1 133 " model vdw 2.275 3.120 nonbonded pdb=" O TRPAP1 91 " pdb=" OH TYRAP1 98 " model vdw 2.282 3.040 nonbonded pdb=" OD2 ASPAP1 592 " pdb=" NH2AARGAP1 595 " model vdw 2.283 3.120 nonbonded pdb=" OG SERAP1 302 " pdb=" O GLYAP1 307 " model vdw 2.285 3.040 ... (remaining 85556 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 Found NCS groups: ncs_group { reference = (chain 'AP1' and (resid 26 through 118 or resid 120 through 142 or (resid 143 th \ rough 144 and (name N or name CA or name C or name O or name CB )) or resid 145 \ through 372 or resid 374 through 518 or (resid 519 and (name N or name CA or nam \ e C or name O or name CB )) or resid 520 through 594 or resid 596 through 801)) selection = (chain 'BP1' and (resid 26 through 45 or (resid 46 and (name N or name CA or nam \ e C or name O or name CB )) or resid 47 through 118 or resid 120 through 205 or \ resid 220 through 372 or resid 374 through 432 or (resid 433 and (name N or name \ CA or name C or name O or name CB )) or resid 434 through 447 or (resid 448 and \ (name N or name CA or name C or name O or name CB )) or resid 449 through 458 o \ r (resid 459 through 460 and (name N or name CA or name C or name O or name CB ) \ ) or resid 461 through 536 or (resid 537 and (name N or name CA or name C or nam \ e O or name CB )) or resid 538 through 594 or resid 596 through 606 or (resid 60 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 608 through \ 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 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: 4.180 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: 0.030 Set scattering table: 0.030 Process input model: 11.360 Find NCS groups from input model: 0.370 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.383 11099 Z= 0.215 Angle : 0.691 15.082 15156 Z= 0.375 Chirality : 0.042 0.134 1597 Planarity : 0.004 0.048 1982 Dihedral : 13.347 89.043 3932 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.96 % Favored : 89.96 % Rotamer: Outliers : 0.18 % Allowed : 3.70 % Favored : 96.12 % 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 are not related in a simple way. whole: -4.12 (0.18), residues: 1388 helix: -2.43 (0.18), residues: 498 sheet: -4.51 (0.70), residues: 10 loop : -3.07 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAP1 128 TYR 0.016 0.001 TYRBP1 28 PHE 0.010 0.001 PHEBP1 483 TRP 0.014 0.001 TRPAP1 149 HIS 0.002 0.001 HISBP1 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (11097) covalent geometry : angle 0.69122 / 0.38 (15156) hydrogen bonds : bond 0.22283 / 15.15 ( 366) hydrogen bonds : angle 7.86747 / 5.63 ( 987) Misc. bond : bond 0.37161 / 18.71 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AP1 141 LEU cc_start: 0.8103 (tp) cc_final: 0.7869 (tt) REVERT: AP1 304 TYR cc_start: 0.8860 (t80) cc_final: 0.8069 (t80) REVERT: AP1 542 ASP cc_start: 0.8235 (m-30) cc_final: 0.7895 (m-30) REVERT: AP1 722 GLN cc_start: 0.8090 (tm-30) cc_final: 0.7881 (tm-30) REVERT: AP1 734 LEU cc_start: 0.8880 (mt) cc_final: 0.8622 (mt) REVERT: BP1 135 TRP cc_start: 0.8901 (m-10) cc_final: 0.8589 (m-10) REVERT: BP1 160 SER cc_start: 0.8771 (m) cc_final: 0.8462 (m) REVERT: BP1 192 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8453 (mm-30) REVERT: BP1 229 TYR cc_start: 0.8195 (m-80) cc_final: 0.7630 (m-10) REVERT: BP1 257 MET cc_start: 0.9160 (mmt) cc_final: 0.8785 (mmm) REVERT: BP1 296 MET cc_start: 0.8700 (mmm) cc_final: 0.8220 (mmm) REVERT: BP1 419 ASP cc_start: 0.8355 (p0) cc_final: 0.7914 (p0) REVERT: BP1 546 LEU cc_start: 0.8684 (mt) cc_final: 0.8299 (tt) REVERT: BP1 561 HIS cc_start: 0.5643 (m-70) cc_final: 0.5357 (m90) REVERT: BP1 562 ASN cc_start: 0.8803 (p0) cc_final: 0.8558 (p0) REVERT: BP1 609 MET cc_start: 0.8742 (mmp) cc_final: 0.8455 (mmt) REVERT: BP1 695 ASP cc_start: 0.8361 (m-30) cc_final: 0.8081 (m-30) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1072 time to fit residues: 19.5957 Evaluate side-chains 79 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.091210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.067739 restraints weight = 44847.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.071999 restraints weight = 17104.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.074963 restraints weight = 9813.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.076883 restraints weight = 6843.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.078301 restraints weight = 5405.300| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 240 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 240 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11099 Z= 0.137 Angle : 0.627 7.423 15156 Z= 0.308 Chirality : 0.042 0.142 1597 Planarity : 0.005 0.051 1982 Dihedral : 5.976 88.422 1519 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.57 % Allowed : 8.87 % Favored : 89.56 % 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 are not related in a simple way. whole: -2.70 (0.20), residues: 1388 helix: -0.97 (0.22), residues: 503 sheet: -4.24 (0.59), residues: 10 loop : -2.40 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAP1 78 TYR 0.031 0.002 TYRAP1 638 PHE 0.012 0.001 PHEAP1 129 TRP 0.018 0.001 TRPAP1 149 HIS 0.003 0.001 HISBP1 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (11097) covalent geometry : angle 0.62672 / 0.31 (15156) hydrogen bonds : bond 0.04941 / 3.36 ( 366) hydrogen bonds : angle 5.32430 / 3.78 ( 987) Misc. bond : bond 0.02201 / 1.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AP1 233 GLU cc_start: 0.8232 (tt0) cc_final: 0.7877 (tt0) REVERT: AP1 296 MET cc_start: 0.9060 (mmm) cc_final: 0.8499 (tpp) REVERT: AP1 304 TYR cc_start: 0.8871 (t80) cc_final: 0.8018 (t80) REVERT: AP1 542 ASP cc_start: 0.8208 (m-30) cc_final: 0.7829 (m-30) REVERT: AP1 609 MET cc_start: 0.8777 (mmm) cc_final: 0.8477 (mmp) REVERT: AP1 709 GLU cc_start: 0.8486 (tt0) cc_final: 0.8130 (tt0) REVERT: AP1 734 LEU cc_start: 0.8826 (mt) cc_final: 0.8579 (mt) REVERT: BP1 127 GLN cc_start: 0.8902 (tt0) cc_final: 0.8621 (tt0) REVERT: BP1 135 TRP cc_start: 0.8720 (m-10) cc_final: 0.8284 (m-10) REVERT: BP1 160 SER cc_start: 0.8494 (m) cc_final: 0.8261 (m) REVERT: BP1 192 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8534 (mm-30) REVERT: BP1 229 TYR cc_start: 0.8161 (m-80) cc_final: 0.7928 (m-10) REVERT: BP1 257 MET cc_start: 0.9109 (mmt) cc_final: 0.8753 (mmm) REVERT: BP1 296 MET cc_start: 0.8653 (mmm) cc_final: 0.8289 (mmm) REVERT: BP1 376 THR cc_start: 0.8797 (p) cc_final: 0.8587 (p) REVERT: BP1 419 ASP cc_start: 0.8277 (p0) cc_final: 0.7860 (p0) REVERT: BP1 561 HIS cc_start: 0.5530 (m-70) cc_final: 0.5279 (m90) REVERT: BP1 562 ASN cc_start: 0.8675 (p0) cc_final: 0.8424 (p0) REVERT: BP1 609 MET cc_start: 0.8707 (mmp) cc_final: 0.8391 (mmt) REVERT: BP1 695 ASP cc_start: 0.8027 (m-30) cc_final: 0.7623 (m-30) outliers start: 15 outliers final: 11 residues processed: 116 average time/residue: 0.0761 time to fit residues: 13.9732 Evaluate side-chains 93 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 35 ASN Chi-restraints excluded: chain AP1 residue 116 HIS Chi-restraints excluded: chain AP1 residue 266 ILE Chi-restraints excluded: chain AP1 residue 319 VAL Chi-restraints excluded: chain BP1 residue 86 THR Chi-restraints excluded: chain BP1 residue 231 ASN Chi-restraints excluded: chain BP1 residue 248 ILE Chi-restraints excluded: chain BP1 residue 266 ILE Chi-restraints excluded: chain BP1 residue 336 LEU Chi-restraints excluded: chain BP1 residue 400 HIS Chi-restraints excluded: chain BP1 residue 687 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 68 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 57 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 63.9228 > 50:) overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.091451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.066192 restraints weight = 64000.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.070736 restraints weight = 21011.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.074018 restraints weight = 11448.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.076275 restraints weight = 7762.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.077642 restraints weight = 5942.759| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 240 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 240 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 11099 Z= 0.137 Angle : 0.587 7.005 15156 Z= 0.283 Chirality : 0.041 0.136 1597 Planarity : 0.004 0.042 1982 Dihedral : 5.758 87.422 1519 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.76 % Allowed : 13.12 % Favored : 85.12 % 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 are not related in a simple way. whole: -2.22 (0.21), residues: 1388 helix: -0.56 (0.22), residues: 519 sheet: -3.95 (0.54), residues: 10 loop : -2.14 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGBP1 78 TYR 0.027 0.001 TYRAP1 638 PHE 0.011 0.001 PHEBP1 252 TRP 0.020 0.001 TRPAP1 161 HIS 0.004 0.001 HISAP1 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (11097) covalent geometry : angle 0.58670 / 0.28 (15156) hydrogen bonds : bond 0.04213 / 2.91 ( 366) hydrogen bonds : angle 4.83800 / 3.42 ( 987) Misc. bond : bond 0.01709 / 0.81 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AP1 233 GLU cc_start: 0.8271 (tt0) cc_final: 0.7490 (tp30) REVERT: AP1 296 MET cc_start: 0.9081 (mmm) cc_final: 0.8508 (tpp) REVERT: AP1 304 TYR cc_start: 0.8896 (t80) cc_final: 0.8077 (t80) REVERT: AP1 542 ASP cc_start: 0.8306 (m-30) cc_final: 0.7959 (m-30) REVERT: AP1 609 MET cc_start: 0.8652 (mmm) cc_final: 0.8380 (mmm) REVERT: AP1 709 GLU cc_start: 0.8521 (tt0) cc_final: 0.8296 (tt0) REVERT: AP1 734 LEU cc_start: 0.8854 (mt) cc_final: 0.8594 (mt) REVERT: BP1 84 MET cc_start: 0.8589 (mtm) cc_final: 0.8360 (ttp) REVERT: BP1 127 GLN cc_start: 0.8928 (tt0) cc_final: 0.8689 (tt0) REVERT: BP1 160 SER cc_start: 0.8551 (m) cc_final: 0.8268 (m) REVERT: BP1 192 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8554 (mm-30) REVERT: BP1 229 TYR cc_start: 0.8089 (m-80) cc_final: 0.7833 (m-10) REVERT: BP1 257 MET cc_start: 0.9100 (mmt) cc_final: 0.8538 (mmm) REVERT: BP1 296 MET cc_start: 0.8691 (mmm) cc_final: 0.8374 (mmm) REVERT: BP1 377 MET cc_start: 0.7599 (mtt) cc_final: 0.7344 (mtt) REVERT: BP1 419 ASP cc_start: 0.8333 (p0) cc_final: 0.7917 (p0) REVERT: BP1 561 HIS cc_start: 0.5501 (m-70) cc_final: 0.5220 (m90) REVERT: BP1 562 ASN cc_start: 0.8695 (p0) cc_final: 0.8447 (p0) REVERT: BP1 609 MET cc_start: 0.8687 (mmp) cc_final: 0.8409 (mmt) REVERT: BP1 623 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: BP1 695 ASP cc_start: 0.8043 (m-30) cc_final: 0.7640 (m-30) outliers start: 17 outliers final: 12 residues processed: 104 average time/residue: 0.0625 time to fit residues: 10.8467 Evaluate side-chains 91 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 35 ASN Chi-restraints excluded: chain AP1 residue 116 HIS Chi-restraints excluded: chain AP1 residue 266 ILE Chi-restraints excluded: chain AP1 residue 319 VAL Chi-restraints excluded: chain AP1 residue 320 VAL Chi-restraints excluded: chain BP1 residue 86 THR Chi-restraints excluded: chain BP1 residue 231 ASN Chi-restraints excluded: chain BP1 residue 248 ILE Chi-restraints excluded: chain BP1 residue 266 ILE Chi-restraints excluded: chain BP1 residue 336 LEU Chi-restraints excluded: chain BP1 residue 400 HIS Chi-restraints excluded: chain BP1 residue 623 GLU Chi-restraints excluded: chain BP1 residue 631 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 82 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 135 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.088484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.064654 restraints weight = 42562.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.068631 restraints weight = 17456.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.071433 restraints weight = 10405.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.073351 restraints weight = 7442.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.074619 restraints weight = 5902.507| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 240 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 240 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.181 11099 Z= 0.253 Angle : 0.651 8.844 15156 Z= 0.311 Chirality : 0.043 0.191 1597 Planarity : 0.004 0.046 1982 Dihedral : 5.818 85.327 1519 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.78 % Favored : 94.15 % Rotamer: Outliers : 2.50 % Allowed : 14.05 % Favored : 83.46 % 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 are not related in a simple way. whole: -1.97 (0.21), residues: 1388 helix: -0.35 (0.22), residues: 518 sheet: -3.74 (0.57), residues: 10 loop : -1.99 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAP1 496 TYR 0.028 0.002 TYRAP1 638 PHE 0.012 0.001 PHEBP1 252 TRP 0.012 0.001 TRPAP1 107 HIS 0.006 0.001 HISBP1 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.25 (11097) covalent geometry : angle 0.65058 / 0.31 (15156) hydrogen bonds : bond 0.04431 / 3.03 ( 366) hydrogen bonds : angle 4.95820 / 3.51 ( 987) Misc. bond : bond 0.16170 / 8.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AP1 296 MET cc_start: 0.9174 (mmm) cc_final: 0.8887 (tpp) REVERT: AP1 304 TYR cc_start: 0.8911 (t80) cc_final: 0.8079 (t80) REVERT: AP1 542 ASP cc_start: 0.8339 (m-30) cc_final: 0.7996 (m-30) REVERT: AP1 709 GLU cc_start: 0.8531 (tt0) cc_final: 0.8296 (tt0) REVERT: AP1 734 LEU cc_start: 0.8912 (mt) cc_final: 0.8656 (mt) REVERT: BP1 84 MET cc_start: 0.8715 (mtm) cc_final: 0.8486 (ttp) REVERT: BP1 160 SER cc_start: 0.8610 (m) cc_final: 0.8341 (m) REVERT: BP1 190 GLN cc_start: 0.8247 (mt0) cc_final: 0.8003 (mt0) REVERT: BP1 192 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8558 (mm-30) REVERT: BP1 229 TYR cc_start: 0.8222 (m-80) cc_final: 0.7955 (m-10) REVERT: BP1 257 MET cc_start: 0.9130 (mmt) cc_final: 0.8334 (mmm) REVERT: BP1 296 MET cc_start: 0.8790 (mmm) cc_final: 0.8351 (mmm) REVERT: BP1 419 ASP cc_start: 0.8340 (p0) cc_final: 0.7958 (p0) REVERT: BP1 561 HIS cc_start: 0.5612 (m-70) cc_final: 0.5298 (m90) REVERT: BP1 562 ASN cc_start: 0.8671 (p0) cc_final: 0.8418 (p0) REVERT: BP1 609 MET cc_start: 0.8775 (mmp) cc_final: 0.8450 (mmt) REVERT: BP1 695 ASP cc_start: 0.8158 (m-30) cc_final: 0.7766 (m-30) outliers start: 25 outliers final: 20 residues processed: 107 average time/residue: 0.0664 time to fit residues: 11.5365 Evaluate side-chains 96 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 35 ASN Chi-restraints excluded: chain AP1 residue 116 HIS Chi-restraints excluded: chain AP1 residue 266 ILE Chi-restraints excluded: chain AP1 residue 319 VAL Chi-restraints excluded: chain AP1 residue 320 VAL Chi-restraints excluded: chain AP1 residue 620 SER Chi-restraints excluded: chain AP1 residue 714 ASP Chi-restraints excluded: chain BP1 residue 86 THR Chi-restraints excluded: chain BP1 residue 189 ASP Chi-restraints excluded: chain BP1 residue 227 LEU Chi-restraints excluded: chain BP1 residue 231 ASN Chi-restraints excluded: chain BP1 residue 248 ILE Chi-restraints excluded: chain BP1 residue 266 ILE Chi-restraints excluded: chain BP1 residue 336 LEU Chi-restraints excluded: chain BP1 residue 400 HIS Chi-restraints excluded: chain BP1 residue 440 ASP Chi-restraints excluded: chain BP1 residue 546 LEU Chi-restraints excluded: chain BP1 residue 631 LEU Chi-restraints excluded: chain BP1 residue 687 VAL Chi-restraints excluded: chain BP1 residue 731 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 42 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.090470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.065943 restraints weight = 55561.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.070326 restraints weight = 19748.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.073435 restraints weight = 11051.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.075566 restraints weight = 7608.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.077031 restraints weight = 5911.585| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 240 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 240 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 11099 Z= 0.183 Angle : 0.597 7.029 15156 Z= 0.286 Chirality : 0.042 0.156 1597 Planarity : 0.004 0.046 1982 Dihedral : 5.748 87.574 1519 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.70 % Favored : 94.22 % Rotamer: Outliers : 1.94 % Allowed : 15.43 % Favored : 82.62 % 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 are not related in a simple way. whole: -1.75 (0.21), residues: 1388 helix: -0.19 (0.22), residues: 518 sheet: -3.53 (0.60), residues: 10 loop : -1.84 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGAP1 496 TYR 0.023 0.001 TYRAP1 638 PHE 0.009 0.001 PHEAP1 167 TRP 0.012 0.001 TRPBP1 341 HIS 0.006 0.001 HISBP1 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.18 (11097) covalent geometry : angle 0.59680 / 0.29 (15156) hydrogen bonds : bond 0.04043 / 2.78 ( 366) hydrogen bonds : angle 4.68241 / 3.31 ( 987) Misc. bond : bond 0.12514 / 6.27 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: AP1 296 MET cc_start: 0.9156 (mmm) cc_final: 0.8871 (tpp) REVERT: AP1 304 TYR cc_start: 0.8916 (t80) cc_final: 0.8122 (t80) REVERT: AP1 542 ASP cc_start: 0.8356 (m-30) cc_final: 0.7989 (m-30) REVERT: AP1 609 MET cc_start: 0.8528 (mmm) cc_final: 0.8252 (mmm) REVERT: AP1 709 GLU cc_start: 0.8510 (tt0) cc_final: 0.8225 (tt0) REVERT: AP1 734 LEU cc_start: 0.8909 (mt) cc_final: 0.8650 (mt) REVERT: BP1 84 MET cc_start: 0.8692 (mtm) cc_final: 0.8480 (ttp) REVERT: BP1 160 SER cc_start: 0.8575 (m) cc_final: 0.8306 (m) REVERT: BP1 190 GLN cc_start: 0.8221 (mt0) cc_final: 0.7956 (mt0) REVERT: BP1 192 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8561 (mm-30) REVERT: BP1 257 MET cc_start: 0.9087 (mmt) cc_final: 0.8854 (mmm) REVERT: BP1 419 ASP cc_start: 0.8341 (p0) cc_final: 0.7956 (p0) REVERT: BP1 561 HIS cc_start: 0.5494 (m-70) cc_final: 0.5169 (m90) REVERT: BP1 562 ASN cc_start: 0.8680 (p0) cc_final: 0.8422 (p0) REVERT: BP1 609 MET cc_start: 0.8737 (mmp) cc_final: 0.8420 (mmt) REVERT: BP1 695 ASP cc_start: 0.8117 (m-30) cc_final: 0.7717 (m-30) outliers start: 19 outliers final: 16 residues processed: 103 average time/residue: 0.0775 time to fit residues: 12.9657 Evaluate side-chains 93 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 35 ASN Chi-restraints excluded: chain AP1 residue 116 HIS Chi-restraints excluded: chain AP1 residue 266 ILE Chi-restraints excluded: chain AP1 residue 319 VAL Chi-restraints excluded: chain AP1 residue 320 VAL Chi-restraints excluded: chain BP1 residue 86 THR Chi-restraints excluded: chain BP1 residue 189 ASP Chi-restraints excluded: chain BP1 residue 231 ASN Chi-restraints excluded: chain BP1 residue 266 ILE Chi-restraints excluded: chain BP1 residue 275 THR Chi-restraints excluded: chain BP1 residue 336 LEU Chi-restraints excluded: chain BP1 residue 400 HIS Chi-restraints excluded: chain BP1 residue 631 LEU Chi-restraints excluded: chain BP1 residue 687 VAL Chi-restraints excluded: chain BP1 residue 697 VAL Chi-restraints excluded: chain BP1 residue 731 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 94 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 80 optimal weight: 0.0570 overall best weight: 1.0900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.092001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.068400 restraints weight = 44940.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.072603 restraints weight = 17665.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.075559 restraints weight = 10284.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.077589 restraints weight = 7195.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.079000 restraints weight = 5640.418| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 240 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 240 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 11099 Z= 0.124 Angle : 0.562 7.514 15156 Z= 0.269 Chirality : 0.041 0.155 1597 Planarity : 0.004 0.049 1982 Dihedral : 5.589 89.910 1519 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.77 % Favored : 95.16 % Rotamer: Outliers : 2.13 % Allowed : 16.45 % Favored : 81.42 % 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 are not related in a simple way. whole: -1.48 (0.21), residues: 1388 helix: 0.06 (0.22), residues: 520 sheet: -3.02 (0.73), residues: 10 loop : -1.71 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGAP1 496 TYR 0.022 0.001 TYRAP1 638 PHE 0.008 0.001 PHEAP1 658 TRP 0.014 0.001 TRPBP1 341 HIS 0.006 0.001 HISBP1 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.12 (11097) covalent geometry : angle 0.56234 / 0.27 (15156) hydrogen bonds : bond 0.03662 / 2.57 ( 366) hydrogen bonds : angle 4.38795 / 3.09 ( 987) Misc. bond : bond 0.06497 / 3.29 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: AP1 105 MET cc_start: 0.8799 (ttm) cc_final: 0.8534 (ttt) REVERT: AP1 296 MET cc_start: 0.9114 (mmm) cc_final: 0.8830 (tpp) REVERT: AP1 304 TYR cc_start: 0.8919 (t80) cc_final: 0.8151 (t80) REVERT: AP1 542 ASP cc_start: 0.8342 (m-30) cc_final: 0.7984 (m-30) REVERT: AP1 609 MET cc_start: 0.8399 (mmm) cc_final: 0.8123 (mmm) REVERT: AP1 734 LEU cc_start: 0.8931 (mt) cc_final: 0.8679 (mt) REVERT: BP1 160 SER cc_start: 0.8504 (m) cc_final: 0.8235 (m) REVERT: BP1 190 GLN cc_start: 0.8235 (mt0) cc_final: 0.7979 (mt0) REVERT: BP1 192 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8562 (mm-30) REVERT: BP1 257 MET cc_start: 0.9029 (mmt) cc_final: 0.8805 (mmm) REVERT: BP1 320 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8841 (m) REVERT: BP1 419 ASP cc_start: 0.8346 (p0) cc_final: 0.7970 (p0) REVERT: BP1 561 HIS cc_start: 0.5395 (m-70) cc_final: 0.5182 (m-70) REVERT: BP1 562 ASN cc_start: 0.8653 (p0) cc_final: 0.8389 (p0) REVERT: BP1 609 MET cc_start: 0.8676 (mmp) cc_final: 0.8391 (mmt) outliers start: 21 outliers final: 15 residues processed: 105 average time/residue: 0.0667 time to fit residues: 11.6111 Evaluate side-chains 94 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 35 ASN Chi-restraints excluded: chain AP1 residue 116 HIS Chi-restraints excluded: chain AP1 residue 266 ILE Chi-restraints excluded: chain AP1 residue 319 VAL Chi-restraints excluded: chain AP1 residue 320 VAL Chi-restraints excluded: chain AP1 residue 377 MET Chi-restraints excluded: chain BP1 residue 86 THR Chi-restraints excluded: chain BP1 residue 189 ASP Chi-restraints excluded: chain BP1 residue 227 LEU Chi-restraints excluded: chain BP1 residue 231 ASN Chi-restraints excluded: chain BP1 residue 266 ILE Chi-restraints excluded: chain BP1 residue 317 ILE Chi-restraints excluded: chain BP1 residue 320 VAL Chi-restraints excluded: chain BP1 residue 336 LEU Chi-restraints excluded: chain BP1 residue 631 LEU Chi-restraints excluded: chain BP1 residue 687 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 38 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.092943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.069380 restraints weight = 39223.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.073467 restraints weight = 16781.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.076360 restraints weight = 10061.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.078356 restraints weight = 7202.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.079744 restraints weight = 5716.460| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 240 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 240 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11099 Z= 0.112 Angle : 0.555 6.753 15156 Z= 0.266 Chirality : 0.040 0.130 1597 Planarity : 0.004 0.050 1982 Dihedral : 5.475 89.075 1519 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.03 % Allowed : 17.01 % Favored : 80.96 % 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 are not related in a simple way. whole: -1.34 (0.22), residues: 1388 helix: 0.16 (0.22), residues: 526 sheet: -2.97 (0.78), residues: 10 loop : -1.62 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGAP1 496 TYR 0.023 0.001 TYRBP1 229 PHE 0.008 0.001 PHEAP1 737 TRP 0.011 0.001 TRPAP1 161 HIS 0.008 0.001 HISBP1 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.11 (11097) covalent geometry : angle 0.55489 / 0.27 (15156) hydrogen bonds : bond 0.03542 / 2.48 ( 366) hydrogen bonds : angle 4.23736 / 2.98 ( 987) Misc. bond : bond 0.04087 / 2.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: AP1 296 MET cc_start: 0.9104 (mmm) cc_final: 0.8668 (tpp) REVERT: AP1 304 TYR cc_start: 0.8916 (t80) cc_final: 0.8180 (t80) REVERT: AP1 542 ASP cc_start: 0.8317 (m-30) cc_final: 0.7976 (m-30) REVERT: AP1 609 MET cc_start: 0.8288 (mmm) cc_final: 0.8011 (mmm) REVERT: AP1 734 LEU cc_start: 0.8930 (mt) cc_final: 0.8655 (mt) REVERT: BP1 160 SER cc_start: 0.8450 (m) cc_final: 0.8229 (m) REVERT: BP1 190 GLN cc_start: 0.8242 (mt0) cc_final: 0.7610 (pt0) REVERT: BP1 192 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8569 (mm-30) REVERT: BP1 257 MET cc_start: 0.9011 (mmt) cc_final: 0.8150 (mmm) REVERT: BP1 419 ASP cc_start: 0.8312 (p0) cc_final: 0.7940 (p0) REVERT: BP1 561 HIS cc_start: 0.5266 (m-70) cc_final: 0.5037 (m-70) REVERT: BP1 562 ASN cc_start: 0.8691 (p0) cc_final: 0.8412 (p0) REVERT: BP1 609 MET cc_start: 0.8632 (mmp) cc_final: 0.8394 (mmt) outliers start: 20 outliers final: 15 residues processed: 104 average time/residue: 0.0642 time to fit residues: 11.1210 Evaluate side-chains 96 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 35 ASN Chi-restraints excluded: chain AP1 residue 116 HIS Chi-restraints excluded: chain AP1 residue 319 VAL Chi-restraints excluded: chain AP1 residue 320 VAL Chi-restraints excluded: chain AP1 residue 377 MET Chi-restraints excluded: chain AP1 residue 714 ASP Chi-restraints excluded: chain BP1 residue 86 THR Chi-restraints excluded: chain BP1 residue 189 ASP Chi-restraints excluded: chain BP1 residue 227 LEU Chi-restraints excluded: chain BP1 residue 231 ASN Chi-restraints excluded: chain BP1 residue 317 ILE Chi-restraints excluded: chain BP1 residue 552 ILE Chi-restraints excluded: chain BP1 residue 631 LEU Chi-restraints excluded: chain BP1 residue 697 VAL Chi-restraints excluded: chain BP1 residue 731 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 118 optimal weight: 9.9990 chunk 28 optimal weight: 0.0170 chunk 74 optimal weight: 1.9990 chunk 93 optimal weight: 0.0570 chunk 5 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 7 optimal weight: 0.0270 chunk 119 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.094640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.070328 restraints weight = 48168.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.074721 restraints weight = 18385.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.077805 restraints weight = 10577.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.079957 restraints weight = 7341.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.081438 restraints weight = 5727.465| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 240 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 240 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 11099 Z= 0.099 Angle : 0.560 9.908 15156 Z= 0.264 Chirality : 0.040 0.131 1597 Planarity : 0.004 0.051 1982 Dihedral : 5.358 88.002 1519 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.48 % Allowed : 17.84 % Favored : 80.68 % 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 are not related in a simple way. whole: -1.22 (0.22), residues: 1388 helix: 0.28 (0.22), residues: 531 sheet: -1.45 (1.00), residues: 20 loop : -1.59 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAP1 496 TYR 0.021 0.001 TYRAP1 638 PHE 0.007 0.001 PHEAP1 737 TRP 0.017 0.001 TRPBP1 321 HIS 0.007 0.001 HISBP1 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 (11097) covalent geometry : angle 0.55980 / 0.26 (15156) hydrogen bonds : bond 0.03332 / 2.38 ( 366) hydrogen bonds : angle 4.07331 / 2.86 ( 987) Misc. bond : bond 0.00412 / 0.21 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AP1 304 TYR cc_start: 0.8922 (t80) cc_final: 0.8182 (t80) REVERT: AP1 542 ASP cc_start: 0.8295 (m-30) cc_final: 0.7979 (m-30) REVERT: AP1 609 MET cc_start: 0.8260 (mmm) cc_final: 0.7992 (mmm) REVERT: AP1 734 LEU cc_start: 0.8944 (mt) cc_final: 0.8684 (mt) REVERT: BP1 160 SER cc_start: 0.8473 (m) cc_final: 0.8178 (m) REVERT: BP1 190 GLN cc_start: 0.8244 (mt0) cc_final: 0.7603 (pt0) REVERT: BP1 192 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8591 (mm-30) REVERT: BP1 419 ASP cc_start: 0.8297 (p0) cc_final: 0.7912 (p0) REVERT: BP1 561 HIS cc_start: 0.5196 (m-70) cc_final: 0.4960 (m-70) REVERT: BP1 562 ASN cc_start: 0.8693 (p0) cc_final: 0.8406 (p0) REVERT: BP1 732 MET cc_start: 0.8625 (tpt) cc_final: 0.8302 (mmm) outliers start: 14 outliers final: 13 residues processed: 103 average time/residue: 0.0718 time to fit residues: 12.1340 Evaluate side-chains 95 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 116 HIS Chi-restraints excluded: chain AP1 residue 319 VAL Chi-restraints excluded: chain AP1 residue 320 VAL Chi-restraints excluded: chain AP1 residue 377 MET Chi-restraints excluded: chain BP1 residue 86 THR Chi-restraints excluded: chain BP1 residue 161 TRP Chi-restraints excluded: chain BP1 residue 189 ASP Chi-restraints excluded: chain BP1 residue 227 LEU Chi-restraints excluded: chain BP1 residue 231 ASN Chi-restraints excluded: chain BP1 residue 317 ILE Chi-restraints excluded: chain BP1 residue 552 ILE Chi-restraints excluded: chain BP1 residue 623 GLU Chi-restraints excluded: chain BP1 residue 731 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 110 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 70 optimal weight: 0.0030 chunk 32 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.094672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.069677 restraints weight = 57047.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.074166 restraints weight = 20184.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.077360 restraints weight = 11316.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.079557 restraints weight = 7782.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.081155 restraints weight = 6032.377| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 240 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 240 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11099 Z= 0.101 Angle : 0.562 9.550 15156 Z= 0.264 Chirality : 0.040 0.132 1597 Planarity : 0.004 0.050 1982 Dihedral : 5.299 88.143 1519 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.48 % Allowed : 17.93 % Favored : 80.59 % 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 are not related in a simple way. whole: -1.08 (0.22), residues: 1388 helix: 0.42 (0.22), residues: 536 sheet: -2.81 (0.72), residues: 10 loop : -1.52 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAP1 496 TYR 0.021 0.001 TYRAP1 638 PHE 0.007 0.001 PHEAP1 737 TRP 0.013 0.001 TRPBP1 149 HIS 0.005 0.001 HISBP1 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.10 (11097) covalent geometry : angle 0.56179 / 0.26 (15156) hydrogen bonds : bond 0.03300 / 2.34 ( 366) hydrogen bonds : angle 4.00442 / 2.81 ( 987) Misc. bond : bond 0.00437 / 0.22 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: AP1 296 MET cc_start: 0.9278 (mmm) cc_final: 0.8558 (tpp) REVERT: AP1 304 TYR cc_start: 0.8915 (t80) cc_final: 0.8192 (t80) REVERT: AP1 542 ASP cc_start: 0.8314 (m-30) cc_final: 0.8003 (m-30) REVERT: AP1 734 LEU cc_start: 0.8941 (mt) cc_final: 0.8661 (mt) REVERT: BP1 160 SER cc_start: 0.8483 (m) cc_final: 0.8250 (m) REVERT: BP1 178 PHE cc_start: 0.7025 (t80) cc_final: 0.6791 (t80) REVERT: BP1 190 GLN cc_start: 0.8251 (mt0) cc_final: 0.7620 (pt0) REVERT: BP1 192 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8583 (mm-30) REVERT: BP1 419 ASP cc_start: 0.8278 (p0) cc_final: 0.7772 (p0) REVERT: BP1 561 HIS cc_start: 0.5163 (m-70) cc_final: 0.4926 (m-70) REVERT: BP1 562 ASN cc_start: 0.8707 (p0) cc_final: 0.8410 (p0) REVERT: BP1 695 ASP cc_start: 0.8453 (m-30) cc_final: 0.8193 (m-30) REVERT: BP1 732 MET cc_start: 0.8670 (tpt) cc_final: 0.8387 (mmm) outliers start: 14 outliers final: 13 residues processed: 99 average time/residue: 0.0686 time to fit residues: 11.2377 Evaluate side-chains 94 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 116 HIS Chi-restraints excluded: chain AP1 residue 319 VAL Chi-restraints excluded: chain AP1 residue 320 VAL Chi-restraints excluded: chain AP1 residue 377 MET Chi-restraints excluded: chain BP1 residue 86 THR Chi-restraints excluded: chain BP1 residue 161 TRP Chi-restraints excluded: chain BP1 residue 189 ASP Chi-restraints excluded: chain BP1 residue 227 LEU Chi-restraints excluded: chain BP1 residue 231 ASN Chi-restraints excluded: chain BP1 residue 317 ILE Chi-restraints excluded: chain BP1 residue 552 ILE Chi-restraints excluded: chain BP1 residue 623 GLU Chi-restraints excluded: chain BP1 residue 731 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 82 optimal weight: 0.0980 chunk 112 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.090874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.066059 restraints weight = 51632.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.070384 restraints weight = 19240.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.073367 restraints weight = 10960.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.075504 restraints weight = 7623.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.076949 restraints weight = 5936.796| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 240 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 240 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 11099 Z= 0.200 Angle : 0.616 9.390 15156 Z= 0.291 Chirality : 0.042 0.164 1597 Planarity : 0.004 0.049 1982 Dihedral : 5.455 89.596 1519 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.85 % Allowed : 17.74 % Favored : 80.41 % 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 are not related in a simple way. whole: -1.01 (0.22), residues: 1388 helix: 0.50 (0.23), residues: 529 sheet: -2.98 (0.72), residues: 10 loop : -1.47 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAP1 496 TYR 0.023 0.001 TYRAP1 638 PHE 0.009 0.001 PHEAP1 183 TRP 0.015 0.001 TRPAP1 149 HIS 0.005 0.001 HISBP1 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (11097) covalent geometry : angle 0.61583 / 0.29 (15156) hydrogen bonds : bond 0.03772 / 2.61 ( 366) hydrogen bonds : angle 4.19730 / 2.94 ( 987) Misc. bond : bond 0.11802 / 5.89 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: AP1 296 MET cc_start: 0.9325 (mmm) cc_final: 0.8572 (tpp) REVERT: AP1 304 TYR cc_start: 0.8929 (t80) cc_final: 0.8206 (t80) REVERT: AP1 542 ASP cc_start: 0.8358 (m-30) cc_final: 0.8022 (m-30) REVERT: AP1 734 LEU cc_start: 0.8965 (mt) cc_final: 0.8683 (mt) REVERT: BP1 105 MET cc_start: 0.8499 (ttm) cc_final: 0.8236 (mtt) REVERT: BP1 160 SER cc_start: 0.8536 (m) cc_final: 0.8302 (m) REVERT: BP1 161 TRP cc_start: 0.8470 (OUTLIER) cc_final: 0.5071 (t60) REVERT: BP1 178 PHE cc_start: 0.7238 (t80) cc_final: 0.7007 (t80) REVERT: BP1 190 GLN cc_start: 0.8241 (mt0) cc_final: 0.7576 (pt0) REVERT: BP1 192 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8554 (mm-30) REVERT: BP1 419 ASP cc_start: 0.8287 (p0) cc_final: 0.7879 (p0) REVERT: BP1 562 ASN cc_start: 0.8692 (p0) cc_final: 0.8414 (p0) REVERT: BP1 609 MET cc_start: 0.8774 (mmp) cc_final: 0.8404 (mmt) REVERT: BP1 732 MET cc_start: 0.8782 (tpt) cc_final: 0.8439 (mmm) outliers start: 18 outliers final: 13 residues processed: 95 average time/residue: 0.0803 time to fit residues: 12.6074 Evaluate side-chains 92 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 35 ASN Chi-restraints excluded: chain AP1 residue 116 HIS Chi-restraints excluded: chain AP1 residue 266 ILE Chi-restraints excluded: chain AP1 residue 319 VAL Chi-restraints excluded: chain AP1 residue 320 VAL Chi-restraints excluded: chain AP1 residue 620 SER Chi-restraints excluded: chain BP1 residue 86 THR Chi-restraints excluded: chain BP1 residue 161 TRP Chi-restraints excluded: chain BP1 residue 189 ASP Chi-restraints excluded: chain BP1 residue 227 LEU Chi-restraints excluded: chain BP1 residue 231 ASN Chi-restraints excluded: chain BP1 residue 317 ILE Chi-restraints excluded: chain BP1 residue 420 MET Chi-restraints excluded: chain BP1 residue 731 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 46 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 132 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.093781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.068891 restraints weight = 61742.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.073465 restraints weight = 20891.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.076709 restraints weight = 11431.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.078975 restraints weight = 7734.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.080538 restraints weight = 5915.885| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 240 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 240 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11099 Z= 0.114 Angle : 0.581 11.431 15156 Z= 0.271 Chirality : 0.040 0.131 1597 Planarity : 0.004 0.051 1982 Dihedral : 5.374 88.459 1519 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.39 % Allowed : 18.39 % Favored : 80.22 % 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 are not related in a simple way. whole: -0.99 (0.22), residues: 1388 helix: 0.50 (0.22), residues: 536 sheet: -2.85 (0.72), residues: 10 loop : -1.46 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGAP1 496 TYR 0.021 0.001 TYRAP1 638 PHE 0.011 0.001 PHEAP1 183 TRP 0.017 0.001 TRPAP1 149 HIS 0.008 0.001 HISBP1 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.11 (11097) covalent geometry : angle 0.58096 / 0.27 (15156) hydrogen bonds : bond 0.03426 / 2.41 ( 366) hydrogen bonds : angle 4.04223 / 2.83 ( 987) Misc. bond : bond 0.05843 / 2.93 ( 2) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 1757.39 seconds wall clock time: 30 minutes 46.44 seconds (1846.44 seconds total)