Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 20:56:06 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a2i_11625/12_2021/7a2i_11625_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a2i_11625/12_2021/7a2i_11625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a2i_11625/12_2021/7a2i_11625.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a2i_11625/12_2021/7a2i_11625.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a2i_11625/12_2021/7a2i_11625_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a2i_11625/12_2021/7a2i_11625_updated.pdb" } resolution = 3.3 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 9196 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4249 Classifications: {'peptide': 563} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 30, 'TRANS': 532} Chain breaks: 4 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 9, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 4947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 4947 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1, 'peptide': 654} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 42, 'TRANS': 611, None: 1} Not linked: pdbres="VAL B 739 " pdbres="HEM B 801 " Chain breaks: 4 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 10, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 84 Time building chain proxies: 5.03, per 1000 atoms: 0.55 Number of scatterers: 9196 At special positions: 0 Unit cell: (83, 96.28, 124.5, 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 1 26.01 S 33 16.00 O 1689 8.00 N 1601 7.00 C 5872 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 - 3.50 Amimo acid : False - 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: 3.34 Conformation dependent library (CDL) restraints added in 1.5 seconds 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2210 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 3 sheets defined 43.5% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 73 through 85 removed outlier: 3.989A pdb=" N ARG A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 149 through 155 removed outlier: 4.410A pdb=" N LYS A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 175 removed outlier: 4.192A pdb=" N VAL A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 255 Processing helix chain 'A' and resid 259 through 268 Processing helix chain 'A' and resid 332 through 336 Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 388 through 399 removed outlier: 4.205A pdb=" N ARG A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TRP A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 417 removed outlier: 3.519A pdb=" N ALA A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 425 No H-bonds generated for 'chain 'A' and resid 423 through 425' Processing helix chain 'A' and resid 455 through 462 removed outlier: 3.573A pdb=" N SER A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 480 removed outlier: 3.570A pdb=" N ALA A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 530 removed outlier: 3.655A pdb=" N ARG A 519 " --> pdb=" O ARG A 515 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN A 525 " --> pdb=" O LEU A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 559 removed outlier: 4.321A pdb=" N VAL A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 586 removed outlier: 4.515A pdb=" N VAL A 586 " --> pdb=" O GLU A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 595 No H-bonds generated for 'chain 'A' and resid 593 through 595' Processing helix chain 'A' and resid 606 through 616 Processing helix chain 'A' and resid 621 through 634 removed outlier: 3.812A pdb=" N VAL A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 656 through 662 Processing helix chain 'A' and resid 696 through 700 Processing helix chain 'A' and resid 702 through 711 removed outlier: 4.336A pdb=" N LEU A 707 " --> pdb=" O GLU A 703 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 710 " --> pdb=" O ALA A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 68 through 70 No H-bonds generated for 'chain 'B' and resid 68 through 70' Processing helix chain 'B' and resid 73 through 83 removed outlier: 3.662A pdb=" N GLU B 82 " --> pdb=" O ARG B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 143 through 147 Processing helix chain 'B' and resid 149 through 155 removed outlier: 4.410A pdb=" N LYS B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR B 155 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 176 removed outlier: 4.181A pdb=" N VAL B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 253 removed outlier: 3.975A pdb=" N VAL B 246 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 269 Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 331 through 336 removed outlier: 3.505A pdb=" N ILE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 385 removed outlier: 4.101A pdb=" N LEU B 384 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 399 removed outlier: 4.012A pdb=" N ILE B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU B 399 " --> pdb=" O ARG B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 416 removed outlier: 3.713A pdb=" N ALA B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 425 No H-bonds generated for 'chain 'B' and resid 423 through 425' Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 455 through 463 removed outlier: 3.694A pdb=" N SER B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 481 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 500 through 503 No H-bonds generated for 'chain 'B' and resid 500 through 503' Processing helix chain 'B' and resid 514 through 531 removed outlier: 4.280A pdb=" N ARG B 519 " --> pdb=" O ARG B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 559 removed outlier: 3.542A pdb=" N VAL B 544 " --> pdb=" O PHE B 540 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 578 No H-bonds generated for 'chain 'B' and resid 576 through 578' Processing helix chain 'B' and resid 581 through 587 removed outlier: 3.642A pdb=" N ALA B 585 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL B 586 " --> pdb=" O GLU B 582 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 581 through 587' Processing helix chain 'B' and resid 593 through 595 No H-bonds generated for 'chain 'B' and resid 593 through 595' Processing helix chain 'B' and resid 606 through 616 Processing helix chain 'B' and resid 621 through 634 removed outlier: 3.659A pdb=" N VAL B 633 " --> pdb=" O GLY B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 655 through 661 removed outlier: 4.011A pdb=" N VAL B 659 " --> pdb=" O ASP B 656 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN B 660 " --> pdb=" O PHE B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 711 removed outlier: 3.912A pdb=" N VAL B 710 " --> pdb=" O ALA B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 734 removed outlier: 3.730A pdb=" N LEU B 734 " --> pdb=" O LYS B 730 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 667 through 670 Processing sheet with id= B, first strand: chain 'B' and resid 342 through 344 Processing sheet with id= C, first strand: chain 'B' and resid 667 through 670 removed outlier: 3.598A pdb=" N GLY B 680 " --> pdb=" O TRP B 689 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP B 689 " --> pdb=" O GLY B 680 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASP B 682 " --> pdb=" O VAL B 687 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL B 687 " --> pdb=" O ASP B 682 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 771 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: 2.19 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.39: 3853 1.39 - 1.56: 5516 1.56 - 1.72: 0 1.72 - 1.88: 62 1.88 - 2.05: 4 Bond restraints: 9435 Sorted by residual: bond pdb=" N LEU B 336 " pdb=" CA LEU B 336 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.35e-02 5.49e+03 5.84e+00 bond pdb=" N ARG B 385 " pdb=" CA ARG B 385 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.42e-02 4.96e+03 4.47e+00 bond pdb=" N ILE B 335 " pdb=" CA ILE B 335 " ideal model delta sigma weight residual 1.461 1.486 -0.025 1.17e-02 7.31e+03 4.41e+00 bond pdb=" C TRP A 39 " pdb=" N PRO A 40 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.20e-02 6.94e+03 2.08e+00 bond pdb=" N VAL B 645 " pdb=" CA VAL B 645 " ideal model delta sigma weight residual 1.474 1.456 0.018 1.57e-02 4.06e+03 1.36e+00 ... (remaining 9430 not shown) Histogram of bond angle deviations from ideal: 89.30 - 107.20: 401 107.20 - 125.10: 12187 125.10 - 143.00: 274 143.00 - 160.90: 0 160.90 - 178.80: 2 Bond angle restraints: 12864 Sorted by residual: angle pdb=" CA ILE B 335 " pdb=" C ILE B 335 " pdb=" O ILE B 335 " ideal model delta sigma weight residual 121.17 117.19 3.98 1.06e+00 8.90e-01 1.41e+01 angle pdb=" C LEU B 336 " pdb=" N TYR B 337 " pdb=" CA TYR B 337 " ideal model delta sigma weight residual 122.49 117.05 5.44 1.57e+00 4.06e-01 1.20e+01 angle pdb=" N TRP B 341 " pdb=" CA TRP B 341 " pdb=" C TRP B 341 " ideal model delta sigma weight residual 110.91 114.92 -4.01 1.17e+00 7.31e-01 1.17e+01 angle pdb=" N ARG B 385 " pdb=" CA ARG B 385 " pdb=" C ARG B 385 " ideal model delta sigma weight residual 114.12 109.96 4.16 1.39e+00 5.18e-01 8.97e+00 angle pdb=" CB MET A 126 " pdb=" CG MET A 126 " pdb=" SD MET A 126 " ideal model delta sigma weight residual 112.70 121.34 -8.64 3.00e+00 1.11e-01 8.29e+00 ... (remaining 12859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 5056 17.69 - 35.37: 381 35.37 - 53.06: 50 53.06 - 70.74: 11 70.74 - 88.43: 8 Dihedral angle restraints: 5506 sinusoidal: 2057 harmonic: 3449 Sorted by residual: dihedral pdb=" CG ARG B 425 " pdb=" CD ARG B 425 " pdb=" NE ARG B 425 " pdb=" CZ ARG B 425 " ideal model delta sinusoidal sigma weight residual 180.00 -135.66 -44.34 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CB GLU B 289 " pdb=" CG GLU B 289 " pdb=" CD GLU B 289 " pdb=" OE1 GLU B 289 " ideal model delta sinusoidal sigma weight residual 0.00 -88.43 88.43 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" C1A HEM B 801 " pdb=" C2A HEM B 801 " pdb=" CAA HEM B 801 " pdb=" CBA HEM B 801 " ideal model delta sinusoidal sigma weight residual 0.00 64.28 -64.28 2 2.00e+01 2.50e-03 9.74e+00 ... (remaining 5503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1072 0.047 - 0.093: 271 0.093 - 0.139: 43 0.139 - 0.186: 0 0.186 - 0.232: 1 Chirality restraints: 1387 Sorted by residual: chirality pdb=" CA ARG B 385 " pdb=" N ARG B 385 " pdb=" C ARG B 385 " pdb=" CB ARG B 385 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA MET A 126 " pdb=" N MET A 126 " pdb=" C MET A 126 " pdb=" CB MET A 126 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA VAL B 442 " pdb=" N VAL B 442 " pdb=" C VAL B 442 " pdb=" CB VAL B 442 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 1384 not shown) Planarity restraints: 1680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 384 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C LEU B 384 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU B 384 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG B 385 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 99 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO A 100 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 100 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 100 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 604 " -0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO B 605 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 605 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 605 " -0.020 5.00e-02 4.00e+02 ... (remaining 1677 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1830 2.77 - 3.30: 9040 3.30 - 3.83: 14330 3.83 - 4.37: 16941 4.37 - 4.90: 29199 Nonbonded interactions: 71340 Sorted by model distance: nonbonded pdb=" O MET B 420 " pdb=" NH1 ARG B 425 " model vdw 2.232 2.520 nonbonded pdb=" OE2 GLU B 506 " pdb=" OH TYR B 638 " model vdw 2.259 2.440 nonbonded pdb=" OH TYR A 337 " pdb=" OG1 THR A 394 " model vdw 2.291 2.440 nonbonded pdb=" OD1 ASP A 406 " pdb=" NZ LYS A 410 " model vdw 2.294 2.520 nonbonded pdb=" OE1 GLN A 88 " pdb=" NE1 TRP A 90 " model vdw 2.295 2.520 ... (remaining 71335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 39 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 through 45 or (resid 46 and (name N or nam \ e CA or name C or name O or name CB )) or resid 47 through 78 or (resid 79 and ( \ name N or name CA or name C or name O or name CB )) or resid 80 or (resid 81 and \ (name N or name CA or name C or name O or name CB )) or resid 82 through 126 or \ (resid 127 and (name N or name CA or name C or name O or name CB )) or resid 12 \ 8 through 140 or (resid 141 through 144 and (name N or name CA or name C or name \ O or name CB )) or resid 145 through 188 or (resid 189 through 190 and (name N \ or name CA or name C or name O or name CB )) or resid 191 through 343 or (resid \ 344 through 346 and (name N or name CA or name C or name O or name CB )) or resi \ d 376 through 379 or (resid 380 through 383 and (name N or name CA or name C or \ name O or name CB )) or resid 384 through 391 or (resid 392 through 393 and (nam \ e N or name CA or name C or name O or name CB )) or resid 394 through 399 or (re \ sid 400 and (name N or name CA or name C or name O or name CB )) or resid 401 or \ (resid 402 and (name N or name CA or name C or name O or name CB )) or resid 40 \ 3 through 441 or (resid 442 and (name N or name CA or name C or name O or name C \ B )) or resid 443 through 473 or (resid 474 and (name N or name CA or name C or \ name O or name CB )) or resid 475 through 480 or (resid 481 and (name N or name \ CA or name C or name O or name CB )) or resid 482 through 521 or (resid 522 and \ (name N or name CA or name C or name O or name CB )) or resid 523 through 561 or \ (resid 562 and (name N or name CA or name C or name O or name CB )) or resid 56 \ 3 through 571 or (resid 572 through 574 and (name N or name CA or name C or name \ O or name CB )) or resid 575 through 587 or (resid 588 and (name N or name CA o \ r name C or name O or name CB )) or resid 589 or (resid 590 through 591 and (nam \ e N or name CA or name C or name O or name CB )) or resid 592 through 609 or (re \ sid 610 and (name N or name CA or name C or name O or name CB )) or resid 611 th \ rough 622 or (resid 623 and (name N or name CA or name C or name O or name CB )) \ or resid 624 through 674 or (resid 675 and (name N or name CA or name C or name \ O or name CB )) or resid 676 or (resid 677 and (name N or name CA or name C or \ name O or name CB )) or resid 678 through 686 or (resid 687 through 688 and (nam \ e N or name CA or name C or name O or name CB )) or resid 689 through 713 or (re \ sid 714 and (name N or name CA or name C or name O or name CB )) or resid 715 th \ rough 737 or (resid 738 through 739 and (name N or name CA or name C or name O o \ r name CB )))) selection = (chain 'B' and (resid 39 through 55 or (resid 56 and (name N or name CA or name \ C or name O or name CB )) or resid 57 through 77 or (resid 78 through 79 and (na \ me N or name CA or name C or name O or name CB )) or resid 80 through 93 or (res \ id 94 and (name N or name CA or name C or name O or name CB )) or resid 95 throu \ gh 118 or (resid 119 and (name N or name CA or name C or name O or name CB )) or \ resid 120 through 128 or resid 138 through 146 or (resid 147 and (name N or nam \ e CA or name C or name O or name CB )) or resid 148 through 173 or (resid 174 th \ rough 175 and (name N or name CA or name C or name O or name CB )) or resid 176 \ through 189 or (resid 190 and (name N or name CA or name C or name O or name CB \ )) or resid 191 through 193 or (resid 194 and (name N or name CA or name C or na \ me O or name CB )) or resid 241 through 246 or (resid 247 and (name N or name CA \ or name C or name O or name CB )) or resid 248 through 257 or (resid 258 throug \ h 259 and (name N or name CA or name C or name O or name CB )) or resid 260 thro \ ugh 261 or (resid 262 through 264 and (name N or name CA or name C or name O or \ name CB )) or resid 265 through 270 or resid 325 or (resid 326 through 327 and ( \ name N or name CA or name C or name O or name CB )) or resid 328 or (resid 329 a \ nd (name N or name CA or name C or name O or name CB )) or resid 330 through 332 \ or (resid 333 through 334 and (name N or name CA or name C or name O or name CB \ )) or resid 335 through 341 or (resid 342 through 346 and (name N or name CA or \ name C or name O or name CB )) or resid 376 through 392 or (resid 393 and (name \ N or name CA or name C or name O or name CB )) or resid 394 through 432 or (res \ id 433 and (name N or name CA or name C or name O or name CB )) or resid 434 thr \ ough 502 or (resid 503 and (name N or name CA or name C or name O or name CB )) \ or resid 504 through 536 or (resid 537 and (name N or name CA or name C or name \ O or name CB )) or resid 538 through 560 or (resid 561 through 562 and (name N o \ r name CA or name C or name O or name CB )) or resid 563 through 567 or (resid 5 \ 68 and (name N or name CA or name C or name O or name CB )) or resid 569 through \ 655 or (resid 656 and (name N or name CA or name C or name O or name CB )) or r \ esid 657 through 661 or (resid 662 and (name N or name CA or name C or name O or \ name CB )) or resid 663 through 687 or (resid 688 and (name N or name CA or nam \ e C or name O or name CB )) or resid 689 through 693 or (resid 694 and (name N o \ r name CA or name C or name O or name CB )) or resid 695 through 716 or (resid 7 \ 17 and (name N or name CA or name C or name O or name CB )) or resid 718 through \ 739)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 33 5.16 5 C 5872 2.51 5 N 1601 2.21 5 O 1689 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic Write .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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.860 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.070 Process input model: 24.370 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 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:2.550 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 33.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 9435 Z= 0.254 Angle : 0.618 8.640 12864 Z= 0.347 Chirality : 0.041 0.232 1387 Planarity : 0.004 0.036 1680 Dihedral : 12.868 88.426 3296 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.24), residues: 1197 helix: -0.12 (0.24), residues: 493 sheet: -3.56 (1.25), residues: 17 loop : -2.22 (0.23), residues: 687 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.096 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2091 time to fit residues: 14.7766 Evaluate side-chains 38 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.022 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.0170 chunk 70 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- 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: 0.8380 moved from start: 0.0629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 9435 Z= 0.149 Angle : 0.481 6.313 12864 Z= 0.236 Chirality : 0.038 0.134 1387 Planarity : 0.004 0.037 1680 Dihedral : 4.580 64.000 1310 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer Outliers : 0.23 % 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: -1.58 (0.25), residues: 1197 helix: 0.19 (0.24), residues: 499 sheet: -3.09 (1.37), residues: 17 loop : -2.04 (0.24), residues: 681 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 1.060 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 45 average time/residue: 0.2122 time to fit residues: 14.7965 Evaluate side-chains 41 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 1.079 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0818 time to fit residues: 1.5699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 91 optimal weight: 0.0010 chunk 74 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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: 0.8391 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9435 Z= 0.179 Angle : 0.472 6.454 12864 Z= 0.230 Chirality : 0.038 0.135 1387 Planarity : 0.003 0.040 1680 Dihedral : 4.476 64.210 1310 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer Outliers : 0.23 % 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: -1.41 (0.25), residues: 1197 helix: 0.37 (0.24), residues: 503 sheet: -3.62 (1.11), residues: 22 loop : -1.95 (0.24), residues: 672 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 1.059 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 48 average time/residue: 0.1845 time to fit residues: 14.0529 Evaluate side-chains 43 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9435 Z= 0.177 Angle : 0.471 7.157 12864 Z= 0.227 Chirality : 0.038 0.135 1387 Planarity : 0.003 0.039 1680 Dihedral : 4.394 64.341 1310 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer Outliers : 0.11 % 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: 1197 helix: 0.50 (0.24), residues: 508 sheet: -3.54 (1.11), residues: 22 loop : -1.86 (0.24), residues: 667 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 1.110 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 44 average time/residue: 0.1902 time to fit residues: 13.4654 Evaluate side-chains 42 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0828 time to fit residues: 1.5995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 99 optimal weight: 0.0980 chunk 80 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 20.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.8371 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 9435 Z= 0.150 Angle : 0.461 7.718 12864 Z= 0.221 Chirality : 0.038 0.134 1387 Planarity : 0.003 0.040 1680 Dihedral : 4.268 64.335 1310 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 0.23 % 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 (0.25), residues: 1197 helix: 0.60 (0.24), residues: 516 sheet: -3.58 (1.08), residues: 22 loop : -1.77 (0.24), residues: 659 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 1.090 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 47 average time/residue: 0.2091 time to fit residues: 15.3730 Evaluate side-chains 44 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.064 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 117 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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: 0.8377 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 9435 Z= 0.165 Angle : 0.464 7.528 12864 Z= 0.222 Chirality : 0.038 0.135 1387 Planarity : 0.003 0.039 1680 Dihedral : 4.267 64.910 1310 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.25), residues: 1197 helix: 0.79 (0.24), residues: 510 sheet: -3.64 (1.05), residues: 22 loop : -1.67 (0.24), residues: 665 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.973 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 45 average time/residue: 0.1914 time to fit residues: 13.6474 Evaluate side-chains 45 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0720 time to fit residues: 1.5175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 116 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.8367 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 9435 Z= 0.151 Angle : 0.460 8.178 12864 Z= 0.218 Chirality : 0.038 0.135 1387 Planarity : 0.003 0.039 1680 Dihedral : 4.196 64.915 1310 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.25), residues: 1197 helix: 0.90 (0.24), residues: 510 sheet: -3.68 (1.04), residues: 22 loop : -1.58 (0.24), residues: 665 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 1.093 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.1831 time to fit residues: 13.8716 Evaluate side-chains 45 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 1.153 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0952 time to fit residues: 1.6599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 10 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 106 optimal weight: 0.0070 chunk 111 optimal weight: 0.0980 chunk 101 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.3998 ------------------------------------------------------------------------------- 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: 0.8329 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 9435 Z= 0.119 Angle : 0.456 8.921 12864 Z= 0.215 Chirality : 0.037 0.133 1387 Planarity : 0.003 0.040 1680 Dihedral : 4.064 64.993 1310 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.25), residues: 1197 helix: 1.08 (0.24), residues: 512 sheet: -2.73 (1.47), residues: 16 loop : -1.50 (0.24), residues: 669 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 1.291 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 47 average time/residue: 0.1942 time to fit residues: 14.6558 Evaluate side-chains 44 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 1.032 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0891 time to fit residues: 1.6862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.2980 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 85 optimal weight: 0.0050 chunk 33 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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: 0.8327 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 9435 Z= 0.123 Angle : 0.460 11.746 12864 Z= 0.214 Chirality : 0.037 0.134 1387 Planarity : 0.003 0.040 1680 Dihedral : 4.002 65.574 1310 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.25), residues: 1197 helix: 1.24 (0.24), residues: 509 sheet: -2.47 (1.28), residues: 21 loop : -1.42 (0.24), residues: 667 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.104 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1859 time to fit residues: 14.3261 Evaluate side-chains 46 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.5980 chunk 79 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8340 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 9435 Z= 0.143 Angle : 0.462 8.704 12864 Z= 0.218 Chirality : 0.038 0.136 1387 Planarity : 0.003 0.040 1680 Dihedral : 4.029 65.591 1310 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.25), residues: 1197 helix: 1.31 (0.24), residues: 509 sheet: -2.32 (1.31), residues: 21 loop : -1.41 (0.24), residues: 667 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.084 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1911 time to fit residues: 14.9191 Evaluate side-chains 45 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 1.081 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 40 optimal weight: 0.4980 chunk 98 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 84 optimal weight: 0.0980 chunk 5 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.119708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.093607 restraints weight = 20300.648| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.37 r_work: 0.3502 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work: 0.3479 rms_B_bonded: 3.11 restraints_weight: 0.1250 r_work: 0.3466 rms_B_bonded: 3.19 restraints_weight: 0.0625 r_work: 0.3453 rms_B_bonded: 3.31 restraints_weight: 0.0312 r_work: 0.3439 rms_B_bonded: 3.46 restraints_weight: 0.0156 r_work: 0.3425 rms_B_bonded: 3.64 restraints_weight: 0.0078 r_work: 0.3410 rms_B_bonded: 3.86 restraints_weight: 0.0039 r_work: 0.3393 rms_B_bonded: 4.11 restraints_weight: 0.0020 r_work: 0.3376 rms_B_bonded: 4.40 restraints_weight: 0.0010 r_work: 0.3358 rms_B_bonded: 4.72 restraints_weight: 0.0005 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 9435 Z= 0.156 Angle : 0.462 8.495 12864 Z= 0.220 Chirality : 0.038 0.135 1387 Planarity : 0.003 0.039 1680 Dihedral : 4.048 65.401 1310 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.25), residues: 1197 helix: 1.35 (0.24), residues: 509 sheet: -2.30 (1.30), residues: 21 loop : -1.39 (0.24), residues: 667 =============================================================================== Job complete usr+sys time: 1479.37 seconds wall clock time: 28 minutes 40.71 seconds (1720.71 seconds total)