Starting phenix.real_space_refine on Fri Nov 15 11:05:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3b_35148/11_2024/8i3b_35148.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3b_35148/11_2024/8i3b_35148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3b_35148/11_2024/8i3b_35148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3b_35148/11_2024/8i3b_35148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3b_35148/11_2024/8i3b_35148.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3b_35148/11_2024/8i3b_35148.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 52 5.16 5 C 5624 2.51 5 N 1446 2.21 5 O 1518 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8646 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4292 Classifications: {'peptide': 550} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 530} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4292 Classifications: {'peptide': 550} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 530} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.90, per 1000 atoms: 0.68 Number of scatterers: 8646 At special positions: 0 Unit cell: (80.51, 93.79, 122.01, 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) S 52 16.00 P 6 15.00 O 1518 8.00 N 1446 7.00 C 5624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.1 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 54.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 106 through 115 Processing helix chain 'A' and resid 137 through 140 removed outlier: 3.653A pdb=" N LYS A 140 " --> pdb=" O GLN A 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 137 through 140' Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 174 through 181 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 210 through 219 removed outlier: 4.183A pdb=" N SER A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 252 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 311 through 319 removed outlier: 3.890A pdb=" N PHE A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 347 removed outlier: 3.577A pdb=" N THR A 340 " --> pdb=" O ASN A 336 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 381 through 401 removed outlier: 3.594A pdb=" N LEU A 393 " --> pdb=" O GLN A 389 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.637A pdb=" N TRP A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 455 removed outlier: 3.800A pdb=" N LEU A 439 " --> pdb=" O ASP A 435 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 473 removed outlier: 4.027A pdb=" N ARG A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 489 removed outlier: 3.756A pdb=" N ALA A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS A 484 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU A 486 " --> pdb=" O MET A 482 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 506 removed outlier: 3.878A pdb=" N ALA A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 540 removed outlier: 3.627A pdb=" N PHE A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 561 removed outlier: 3.993A pdb=" N THR A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 removed outlier: 4.185A pdb=" N VAL A 579 " --> pdb=" O TRP A 575 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 580 " --> pdb=" O MET A 576 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 575 through 580' Processing helix chain 'A' and resid 581 through 595 removed outlier: 3.807A pdb=" N CYS A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 604 Processing helix chain 'A' and resid 639 through 656 removed outlier: 3.549A pdb=" N LEU A 644 " --> pdb=" O GLY A 640 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 137 through 140 removed outlier: 3.652A pdb=" N LYS B 140 " --> pdb=" O GLN B 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 137 through 140' Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 210 through 219 removed outlier: 4.182A pdb=" N SER B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 252 Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 311 through 319 removed outlier: 3.889A pdb=" N PHE B 315 " --> pdb=" O ASN B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 347 removed outlier: 3.578A pdb=" N THR B 340 " --> pdb=" O ASN B 336 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR B 347 " --> pdb=" O THR B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 357 Processing helix chain 'B' and resid 381 through 401 removed outlier: 3.594A pdb=" N LEU B 393 " --> pdb=" O GLN B 389 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.637A pdb=" N TRP B 425 " --> pdb=" O CYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 455 removed outlier: 3.799A pdb=" N LEU B 439 " --> pdb=" O ASP B 435 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 462 through 473 removed outlier: 4.026A pdb=" N ARG B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 489 removed outlier: 3.756A pdb=" N ALA B 483 " --> pdb=" O SER B 479 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS B 484 " --> pdb=" O TYR B 480 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU B 486 " --> pdb=" O MET B 482 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 489 " --> pdb=" O VAL B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 506 removed outlier: 3.878A pdb=" N ALA B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE B 502 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TRP B 505 " --> pdb=" O THR B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 540 removed outlier: 3.627A pdb=" N PHE B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY B 538 " --> pdb=" O GLY B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 561 removed outlier: 3.994A pdb=" N THR B 549 " --> pdb=" O LYS B 545 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B 552 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL B 553 " --> pdb=" O THR B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 580 removed outlier: 4.185A pdb=" N VAL B 579 " --> pdb=" O TRP B 575 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 580 " --> pdb=" O MET B 576 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 575 through 580' Processing helix chain 'B' and resid 581 through 595 removed outlier: 3.807A pdb=" N CYS B 585 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 604 Processing helix chain 'B' and resid 639 through 656 removed outlier: 3.548A pdb=" N LEU B 644 " --> pdb=" O GLY B 640 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 91 removed outlier: 5.624A pdb=" N ARG A 81 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LYS A 50 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE A 83 " --> pdb=" O ARG A 48 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ARG A 48 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER A 85 " --> pdb=" O CYS A 46 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS A 46 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N VAL A 87 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.221A pdb=" N ALA A 98 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU A 281 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU A 100 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 278 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL A 289 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU A 280 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.242A pdb=" N GLY A 143 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU A 228 " --> pdb=" O VAL A 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 91 removed outlier: 5.623A pdb=" N ARG B 81 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LYS B 50 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE B 83 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ARG B 48 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER B 85 " --> pdb=" O CYS B 46 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N CYS B 46 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N VAL B 87 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.221A pdb=" N ALA B 98 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU B 281 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU B 100 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 278 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL B 289 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU B 280 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.242A pdb=" N GLY B 143 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU B 228 " --> pdb=" O VAL B 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 356 hydrogen bonds defined for protein. 1038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2103 1.33 - 1.45: 1737 1.45 - 1.57: 4894 1.57 - 1.69: 10 1.69 - 1.81: 86 Bond restraints: 8830 Sorted by residual: bond pdb=" C4 ATP B 701 " pdb=" C5 ATP B 701 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.51e+01 bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.33e+01 bond pdb=" C5 ATP A 701 " pdb=" C6 ATP A 701 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.17e+01 bond pdb=" C5 ATP B 701 " pdb=" C6 ATP B 701 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.13e+01 bond pdb=" C5 ATP B 701 " pdb=" N7 ATP B 701 " ideal model delta sigma weight residual 1.387 1.338 0.049 1.00e-02 1.00e+04 2.39e+01 ... (remaining 8825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 11812 3.83 - 7.66: 140 7.66 - 11.49: 24 11.49 - 15.32: 0 15.32 - 19.16: 4 Bond angle restraints: 11980 Sorted by residual: angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 120.71 19.16 1.00e+00 1.00e+00 3.67e+02 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 120.72 19.15 1.00e+00 1.00e+00 3.67e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 120.55 16.28 1.00e+00 1.00e+00 2.65e+02 angle pdb=" PA ATP B 701 " pdb=" O3A ATP B 701 " pdb=" PB ATP B 701 " ideal model delta sigma weight residual 136.83 120.55 16.28 1.00e+00 1.00e+00 2.65e+02 angle pdb=" C5 ATP B 701 " pdb=" C4 ATP B 701 " pdb=" N3 ATP B 701 " ideal model delta sigma weight residual 126.80 118.78 8.02 1.00e+00 1.00e+00 6.43e+01 ... (remaining 11975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4683 18.00 - 36.00: 473 36.00 - 53.99: 48 53.99 - 71.99: 18 71.99 - 89.99: 4 Dihedral angle restraints: 5226 sinusoidal: 2074 harmonic: 3152 Sorted by residual: dihedral pdb=" CA GLY B 104 " pdb=" C GLY B 104 " pdb=" N SER B 105 " pdb=" CA SER B 105 " ideal model delta harmonic sigma weight residual -180.00 -154.46 -25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA GLY A 104 " pdb=" C GLY A 104 " pdb=" N SER A 105 " pdb=" CA SER A 105 " ideal model delta harmonic sigma weight residual -180.00 -154.47 -25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA GLY B 631 " pdb=" C GLY B 631 " pdb=" N ASP B 632 " pdb=" CA ASP B 632 " ideal model delta harmonic sigma weight residual 180.00 -156.31 -23.69 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 5223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1136 0.069 - 0.138: 247 0.138 - 0.208: 31 0.208 - 0.277: 8 0.277 - 0.346: 4 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CB ILE A 129 " pdb=" CA ILE A 129 " pdb=" CG1 ILE A 129 " pdb=" CG2 ILE A 129 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CB ILE B 129 " pdb=" CA ILE B 129 " pdb=" CG1 ILE B 129 " pdb=" CG2 ILE B 129 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CB VAL B 199 " pdb=" CA VAL B 199 " pdb=" CG1 VAL B 199 " pdb=" CG2 VAL B 199 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 1423 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 51 " -0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C ILE A 51 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE A 51 " -0.021 2.00e-02 2.50e+03 pdb=" N HIS A 52 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 51 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.95e+00 pdb=" C ILE B 51 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE B 51 " -0.021 2.00e-02 2.50e+03 pdb=" N HIS B 52 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 169 " 0.043 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO A 170 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " 0.036 5.00e-02 4.00e+02 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1981 2.78 - 3.31: 7582 3.31 - 3.84: 13599 3.84 - 4.37: 16642 4.37 - 4.90: 28822 Nonbonded interactions: 68626 Sorted by model distance: nonbonded pdb=" OG1 THR A 156 " pdb=" OE1 GLU A 159 " model vdw 2.249 3.040 nonbonded pdb=" OG1 THR B 156 " pdb=" OE1 GLU B 159 " model vdw 2.250 3.040 nonbonded pdb=" OH TYR A 578 " pdb=" OD2 ASP A 632 " model vdw 2.295 3.040 nonbonded pdb=" OH TYR B 578 " pdb=" OD2 ASP B 632 " model vdw 2.296 3.040 nonbonded pdb=" OE1 GLU B 469 " pdb=" OH TYR B 475 " model vdw 2.330 3.040 ... (remaining 68621 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 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.580 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 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 : 0.008 0.075 8830 Z= 0.513 Angle : 1.189 19.156 11980 Z= 0.754 Chirality : 0.062 0.346 1426 Planarity : 0.007 0.066 1452 Dihedral : 14.311 89.989 3198 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 1.50 % Allowed : 6.94 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.42 (0.18), residues: 1076 helix: -3.50 (0.13), residues: 614 sheet: -2.64 (0.44), residues: 80 loop : -3.65 (0.24), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 426 HIS 0.013 0.002 HIS B 52 PHE 0.020 0.002 PHE A 499 TYR 0.014 0.002 TYR A 594 ARG 0.003 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8413 (t0) cc_final: 0.8055 (t70) REVERT: A 462 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7553 (mm-30) REVERT: B 231 ASP cc_start: 0.8421 (t0) cc_final: 0.8062 (t70) REVERT: B 462 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7430 (mm-30) REVERT: B 546 LYS cc_start: 0.7629 (mttt) cc_final: 0.7397 (mttm) outliers start: 14 outliers final: 7 residues processed: 137 average time/residue: 0.2423 time to fit residues: 44.6365 Evaluate side-chains 94 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 342 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 112 ASN A 265 HIS A 395 HIS B 52 HIS ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 HIS B 427 HIS B 434 HIS B 567 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8830 Z= 0.183 Angle : 0.599 7.711 11980 Z= 0.315 Chirality : 0.042 0.201 1426 Planarity : 0.005 0.060 1452 Dihedral : 8.571 82.587 1264 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.85 % Allowed : 12.71 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.22), residues: 1076 helix: -1.90 (0.18), residues: 606 sheet: -2.56 (0.55), residues: 60 loop : -3.08 (0.25), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 447 HIS 0.006 0.001 HIS A 52 PHE 0.017 0.001 PHE A 315 TYR 0.012 0.001 TYR B 152 ARG 0.005 0.000 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 1.018 Fit side-chains REVERT: A 152 TYR cc_start: 0.8784 (m-80) cc_final: 0.7987 (m-80) REVERT: A 231 ASP cc_start: 0.8327 (t0) cc_final: 0.7996 (t70) REVERT: A 286 CYS cc_start: 0.7821 (p) cc_final: 0.7381 (p) REVERT: A 293 ARG cc_start: 0.6522 (mmt-90) cc_final: 0.6022 (mmp80) REVERT: A 315 PHE cc_start: 0.7113 (t80) cc_final: 0.6539 (t80) REVERT: A 462 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7278 (mm-30) REVERT: A 492 GLU cc_start: 0.7286 (tp30) cc_final: 0.6189 (tp30) REVERT: A 573 MET cc_start: 0.8542 (ttm) cc_final: 0.8114 (ttm) REVERT: B 152 TYR cc_start: 0.8818 (m-80) cc_final: 0.8044 (m-80) REVERT: B 231 ASP cc_start: 0.8390 (t0) cc_final: 0.8080 (t70) REVERT: B 462 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7294 (mm-30) REVERT: B 492 GLU cc_start: 0.7278 (tp30) cc_final: 0.6203 (tp30) REVERT: B 508 TYR cc_start: 0.7368 (t80) cc_final: 0.7068 (t80) REVERT: B 573 MET cc_start: 0.8523 (ttm) cc_final: 0.8223 (ttm) REVERT: B 645 MET cc_start: 0.7526 (mtt) cc_final: 0.7322 (mtt) outliers start: 8 outliers final: 6 residues processed: 117 average time/residue: 0.2467 time to fit residues: 38.4847 Evaluate side-chains 98 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 280 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 100 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS A 427 HIS B 254 HIS B 273 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8830 Z= 0.332 Angle : 0.647 7.391 11980 Z= 0.332 Chirality : 0.044 0.163 1426 Planarity : 0.005 0.059 1452 Dihedral : 8.455 82.962 1256 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.35 % Allowed : 14.21 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.22), residues: 1076 helix: -1.41 (0.19), residues: 608 sheet: -2.42 (0.55), residues: 60 loop : -2.98 (0.25), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 447 HIS 0.005 0.001 HIS A 265 PHE 0.014 0.002 PHE A 446 TYR 0.010 0.002 TYR A 565 ARG 0.003 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.980 Fit side-chains REVERT: A 152 TYR cc_start: 0.8761 (m-80) cc_final: 0.8054 (m-80) REVERT: A 231 ASP cc_start: 0.8389 (t0) cc_final: 0.8059 (t70) REVERT: A 286 CYS cc_start: 0.7783 (p) cc_final: 0.7409 (p) REVERT: A 462 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7212 (mm-30) REVERT: A 492 GLU cc_start: 0.7272 (tp30) cc_final: 0.6378 (tp30) REVERT: A 573 MET cc_start: 0.8569 (ttm) cc_final: 0.8316 (ttm) REVERT: B 152 TYR cc_start: 0.8787 (m-80) cc_final: 0.8401 (m-80) REVERT: B 231 ASP cc_start: 0.8422 (t0) cc_final: 0.8090 (t70) REVERT: B 286 CYS cc_start: 0.7790 (p) cc_final: 0.7337 (p) REVERT: B 462 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7433 (mm-30) REVERT: B 492 GLU cc_start: 0.7280 (tp30) cc_final: 0.6336 (tp30) REVERT: B 508 TYR cc_start: 0.7428 (t80) cc_final: 0.7170 (t80) REVERT: B 573 MET cc_start: 0.8582 (ttm) cc_final: 0.8323 (ttm) outliers start: 22 outliers final: 18 residues processed: 109 average time/residue: 0.1816 time to fit residues: 29.5266 Evaluate side-chains 105 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 514 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 51 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 67 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8830 Z= 0.217 Angle : 0.564 7.285 11980 Z= 0.292 Chirality : 0.042 0.145 1426 Planarity : 0.004 0.057 1452 Dihedral : 8.179 84.171 1256 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.60 % Allowed : 15.81 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.24), residues: 1076 helix: -0.82 (0.20), residues: 606 sheet: -2.16 (0.57), residues: 60 loop : -2.62 (0.26), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 447 HIS 0.004 0.001 HIS A 219 PHE 0.027 0.001 PHE A 315 TYR 0.006 0.001 TYR A 565 ARG 0.002 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 1.048 Fit side-chains REVERT: A 231 ASP cc_start: 0.8374 (t0) cc_final: 0.8020 (t70) REVERT: A 286 CYS cc_start: 0.7697 (p) cc_final: 0.7341 (p) REVERT: A 409 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7980 (tt) REVERT: A 492 GLU cc_start: 0.7147 (tp30) cc_final: 0.6281 (tp30) REVERT: A 573 MET cc_start: 0.8546 (ttm) cc_final: 0.8293 (ttm) REVERT: B 152 TYR cc_start: 0.8750 (m-80) cc_final: 0.8450 (m-80) REVERT: B 231 ASP cc_start: 0.8400 (t0) cc_final: 0.8081 (t70) REVERT: B 286 CYS cc_start: 0.7777 (p) cc_final: 0.7410 (p) REVERT: B 409 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7875 (tt) REVERT: B 462 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7435 (mm-30) REVERT: B 492 GLU cc_start: 0.7187 (tp30) cc_final: 0.6290 (tp30) REVERT: B 508 TYR cc_start: 0.7437 (t80) cc_final: 0.7228 (t80) REVERT: B 573 MET cc_start: 0.8573 (ttm) cc_final: 0.8355 (ttm) outliers start: 15 outliers final: 11 residues processed: 104 average time/residue: 0.1933 time to fit residues: 29.2550 Evaluate side-chains 101 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 514 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8830 Z= 0.281 Angle : 0.594 7.631 11980 Z= 0.303 Chirality : 0.043 0.154 1426 Planarity : 0.004 0.056 1452 Dihedral : 8.210 83.989 1256 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.88 % Allowed : 16.77 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.24), residues: 1076 helix: -0.65 (0.21), residues: 612 sheet: -1.94 (0.61), residues: 60 loop : -2.48 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 447 HIS 0.005 0.001 HIS A 219 PHE 0.020 0.001 PHE A 315 TYR 0.011 0.001 TYR A 152 ARG 0.001 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.900 Fit side-chains REVERT: A 152 TYR cc_start: 0.8753 (m-80) cc_final: 0.8180 (m-80) REVERT: A 183 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.6241 (mp0) REVERT: A 231 ASP cc_start: 0.8375 (t0) cc_final: 0.8032 (t70) REVERT: A 286 CYS cc_start: 0.7676 (p) cc_final: 0.7331 (p) REVERT: A 409 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7932 (tt) REVERT: A 462 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7242 (mm-30) REVERT: A 482 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7929 (mmm) REVERT: A 492 GLU cc_start: 0.7132 (tp30) cc_final: 0.6265 (tp30) REVERT: B 137 GLN cc_start: 0.8851 (mp10) cc_final: 0.8619 (mp10) REVERT: B 183 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.6218 (mp0) REVERT: B 231 ASP cc_start: 0.8392 (t0) cc_final: 0.8048 (t70) REVERT: B 286 CYS cc_start: 0.7739 (p) cc_final: 0.7470 (p) REVERT: B 409 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7876 (tt) REVERT: B 492 GLU cc_start: 0.7155 (tp30) cc_final: 0.6272 (tp30) outliers start: 27 outliers final: 17 residues processed: 115 average time/residue: 0.1777 time to fit residues: 30.3088 Evaluate side-chains 113 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 514 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 102 optimal weight: 0.3980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8830 Z= 0.318 Angle : 0.615 8.093 11980 Z= 0.313 Chirality : 0.044 0.157 1426 Planarity : 0.004 0.056 1452 Dihedral : 8.295 83.643 1256 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.99 % Allowed : 16.99 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.24), residues: 1076 helix: -0.62 (0.21), residues: 616 sheet: -1.68 (0.63), residues: 62 loop : -2.39 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 447 HIS 0.006 0.001 HIS B 219 PHE 0.031 0.002 PHE A 315 TYR 0.014 0.002 TYR B 152 ARG 0.002 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 1.043 Fit side-chains REVERT: A 97 MET cc_start: 0.6723 (tpt) cc_final: 0.6136 (tpt) REVERT: A 137 GLN cc_start: 0.8825 (mp10) cc_final: 0.8581 (mp10) REVERT: A 152 TYR cc_start: 0.8749 (m-80) cc_final: 0.8545 (m-80) REVERT: A 231 ASP cc_start: 0.8400 (t0) cc_final: 0.7968 (t0) REVERT: A 286 CYS cc_start: 0.7688 (p) cc_final: 0.7476 (p) REVERT: A 409 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7961 (tt) REVERT: A 492 GLU cc_start: 0.7138 (tp30) cc_final: 0.6251 (tp30) REVERT: B 97 MET cc_start: 0.6687 (tpt) cc_final: 0.6122 (tpt) REVERT: B 137 GLN cc_start: 0.8824 (mp10) cc_final: 0.8587 (mp10) REVERT: B 152 TYR cc_start: 0.8776 (m-80) cc_final: 0.8490 (m-80) REVERT: B 231 ASP cc_start: 0.8407 (t0) cc_final: 0.7984 (t0) REVERT: B 286 CYS cc_start: 0.7700 (p) cc_final: 0.7461 (p) REVERT: B 409 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7897 (tt) REVERT: B 462 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7306 (mm-30) REVERT: B 492 GLU cc_start: 0.7172 (tp30) cc_final: 0.6275 (tp30) outliers start: 28 outliers final: 20 residues processed: 119 average time/residue: 0.1848 time to fit residues: 32.0049 Evaluate side-chains 114 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 633 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 0.0070 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8830 Z= 0.168 Angle : 0.539 7.064 11980 Z= 0.277 Chirality : 0.040 0.139 1426 Planarity : 0.004 0.054 1452 Dihedral : 7.938 85.196 1256 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.56 % Allowed : 17.74 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.25), residues: 1076 helix: -0.24 (0.21), residues: 616 sheet: -1.53 (0.68), residues: 60 loop : -2.28 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 447 HIS 0.004 0.000 HIS A 219 PHE 0.030 0.001 PHE A 315 TYR 0.009 0.001 TYR B 152 ARG 0.002 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 1.063 Fit side-chains REVERT: A 97 MET cc_start: 0.6631 (tpt) cc_final: 0.5990 (tpt) REVERT: A 137 GLN cc_start: 0.8844 (mp10) cc_final: 0.8603 (mp10) REVERT: A 152 TYR cc_start: 0.8719 (m-80) cc_final: 0.8505 (m-80) REVERT: A 231 ASP cc_start: 0.8390 (t0) cc_final: 0.8026 (t70) REVERT: A 286 CYS cc_start: 0.7631 (p) cc_final: 0.7328 (p) REVERT: A 409 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7864 (tt) REVERT: A 492 GLU cc_start: 0.7081 (tp30) cc_final: 0.6136 (tp30) REVERT: B 97 MET cc_start: 0.6642 (tpt) cc_final: 0.5994 (tpt) REVERT: B 137 GLN cc_start: 0.8833 (mp10) cc_final: 0.8602 (mp10) REVERT: B 152 TYR cc_start: 0.8723 (m-80) cc_final: 0.8037 (m-80) REVERT: B 231 ASP cc_start: 0.8392 (t0) cc_final: 0.8023 (t70) REVERT: B 286 CYS cc_start: 0.7748 (p) cc_final: 0.7461 (p) REVERT: B 288 PHE cc_start: 0.7534 (t80) cc_final: 0.7296 (t80) REVERT: B 409 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7854 (tt) REVERT: B 462 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7044 (mm-30) REVERT: B 492 GLU cc_start: 0.7135 (tp30) cc_final: 0.6187 (tp30) outliers start: 24 outliers final: 18 residues processed: 118 average time/residue: 0.1752 time to fit residues: 30.9915 Evaluate side-chains 111 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 633 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8830 Z= 0.306 Angle : 0.634 9.303 11980 Z= 0.318 Chirality : 0.044 0.153 1426 Planarity : 0.004 0.055 1452 Dihedral : 7.963 84.221 1256 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.31 % Allowed : 18.06 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.25), residues: 1076 helix: -0.30 (0.21), residues: 614 sheet: -1.48 (0.66), residues: 62 loop : -2.25 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 447 HIS 0.005 0.001 HIS A 219 PHE 0.031 0.001 PHE A 315 TYR 0.010 0.001 TYR B 152 ARG 0.001 0.000 ARG B 470 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 1.078 Fit side-chains REVERT: A 97 MET cc_start: 0.6763 (tpt) cc_final: 0.6214 (tpt) REVERT: A 137 GLN cc_start: 0.8848 (mp10) cc_final: 0.8599 (mp10) REVERT: A 231 ASP cc_start: 0.8387 (t0) cc_final: 0.7953 (t0) REVERT: A 286 CYS cc_start: 0.7684 (p) cc_final: 0.7471 (p) REVERT: A 409 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7943 (tt) REVERT: A 492 GLU cc_start: 0.7103 (tp30) cc_final: 0.6179 (tp30) REVERT: B 97 MET cc_start: 0.6740 (tpt) cc_final: 0.6185 (tpt) REVERT: B 231 ASP cc_start: 0.8390 (t0) cc_final: 0.8030 (t70) REVERT: B 288 PHE cc_start: 0.7646 (t80) cc_final: 0.7389 (t80) REVERT: B 409 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7924 (tt) REVERT: B 492 GLU cc_start: 0.7157 (tp30) cc_final: 0.6204 (tp30) outliers start: 31 outliers final: 20 residues processed: 120 average time/residue: 0.1786 time to fit residues: 31.8473 Evaluate side-chains 113 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 633 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 0.0010 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.0980 chunk 64 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8830 Z= 0.139 Angle : 0.538 8.175 11980 Z= 0.276 Chirality : 0.040 0.139 1426 Planarity : 0.004 0.052 1452 Dihedral : 7.665 86.239 1256 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.03 % Allowed : 19.23 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.25), residues: 1076 helix: 0.08 (0.21), residues: 616 sheet: -1.39 (0.70), residues: 60 loop : -2.14 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 447 HIS 0.003 0.000 HIS A 219 PHE 0.029 0.001 PHE A 315 TYR 0.010 0.001 TYR B 152 ARG 0.001 0.000 ARG B 463 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 1.071 Fit side-chains REVERT: A 97 MET cc_start: 0.6530 (tpt) cc_final: 0.5869 (tpt) REVERT: A 137 GLN cc_start: 0.8834 (mp10) cc_final: 0.8593 (mp10) REVERT: A 152 TYR cc_start: 0.8679 (m-80) cc_final: 0.7578 (m-80) REVERT: A 159 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6123 (mp0) REVERT: A 231 ASP cc_start: 0.8320 (t0) cc_final: 0.7981 (t70) REVERT: A 286 CYS cc_start: 0.7693 (p) cc_final: 0.7433 (p) REVERT: A 409 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7879 (tt) REVERT: A 462 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6877 (mm-30) REVERT: A 492 GLU cc_start: 0.7101 (tp30) cc_final: 0.6192 (tp30) REVERT: A 635 MET cc_start: 0.7998 (ttt) cc_final: 0.7769 (ttm) REVERT: B 97 MET cc_start: 0.6547 (tpt) cc_final: 0.5927 (tpt) REVERT: B 159 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6130 (mp0) REVERT: B 231 ASP cc_start: 0.8318 (t0) cc_final: 0.7992 (t70) REVERT: B 409 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7882 (tt) REVERT: B 492 GLU cc_start: 0.7138 (tp30) cc_final: 0.6230 (tp30) outliers start: 19 outliers final: 15 residues processed: 120 average time/residue: 0.1769 time to fit residues: 31.3581 Evaluate side-chains 110 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 633 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 109 optimal weight: 0.0070 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 0.0980 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8830 Z= 0.232 Angle : 0.591 9.635 11980 Z= 0.298 Chirality : 0.042 0.142 1426 Planarity : 0.004 0.054 1452 Dihedral : 7.620 84.929 1256 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.46 % Allowed : 18.70 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.25), residues: 1076 helix: 0.08 (0.21), residues: 614 sheet: -1.30 (0.70), residues: 60 loop : -2.11 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 447 HIS 0.004 0.000 HIS B 219 PHE 0.029 0.001 PHE A 315 TYR 0.013 0.001 TYR B 152 ARG 0.001 0.000 ARG A 401 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.6743 (tpt) cc_final: 0.6128 (tpt) REVERT: A 152 TYR cc_start: 0.8721 (m-80) cc_final: 0.8503 (m-80) REVERT: A 159 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6140 (mp0) REVERT: A 231 ASP cc_start: 0.8270 (t0) cc_final: 0.7922 (t70) REVERT: A 286 CYS cc_start: 0.7619 (p) cc_final: 0.7369 (p) REVERT: A 291 LYS cc_start: 0.6486 (mppt) cc_final: 0.5840 (ttmm) REVERT: A 409 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7894 (tt) REVERT: A 492 GLU cc_start: 0.7067 (tp30) cc_final: 0.6157 (tp30) REVERT: B 97 MET cc_start: 0.6732 (tpt) cc_final: 0.6113 (tpt) REVERT: B 159 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6139 (mp0) REVERT: B 231 ASP cc_start: 0.8319 (t0) cc_final: 0.7987 (t70) REVERT: B 286 CYS cc_start: 0.7692 (p) cc_final: 0.7373 (p) REVERT: B 288 PHE cc_start: 0.7434 (t80) cc_final: 0.7176 (t80) REVERT: B 409 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7895 (tt) REVERT: B 462 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7142 (mm-30) REVERT: B 492 GLU cc_start: 0.7098 (tp30) cc_final: 0.6174 (tp30) outliers start: 23 outliers final: 16 residues processed: 112 average time/residue: 0.2084 time to fit residues: 34.3638 Evaluate side-chains 110 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 633 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 63 optimal weight: 0.2980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.158546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.118270 restraints weight = 10570.501| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.90 r_work: 0.3327 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8830 Z= 0.194 Angle : 0.579 10.487 11980 Z= 0.289 Chirality : 0.041 0.139 1426 Planarity : 0.004 0.055 1452 Dihedral : 7.591 85.051 1256 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.78 % Allowed : 18.48 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.26), residues: 1076 helix: 0.20 (0.21), residues: 614 sheet: -1.18 (0.71), residues: 60 loop : -2.05 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 447 HIS 0.003 0.000 HIS B 219 PHE 0.029 0.001 PHE A 315 TYR 0.013 0.001 TYR B 152 ARG 0.001 0.000 ARG B 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1876.50 seconds wall clock time: 35 minutes 7.21 seconds (2107.21 seconds total)