Starting phenix.real_space_refine on Tue Mar 3 23:40:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a2i_11625/03_2026/7a2i_11625.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a2i_11625/03_2026/7a2i_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 { model { file = "/net/cci-nas-00/data/ceres_data/7a2i_11625/03_2026/7a2i_11625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a2i_11625/03_2026/7a2i_11625.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7a2i_11625/03_2026/7a2i_11625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a2i_11625/03_2026/7a2i_11625.map" } 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 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= 0.003 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 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. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9196 Number of models: 1 Model: "" Number of chains: 3 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: {'ASP:plan': 9, 'ARG:plan': 2, 'GLU:plan': 5, 'GLN:plan1': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 4904 Classifications: {'peptide': 654} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 42, 'TRANS': 611} 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: {'ARG:plan': 2, 'ASP:plan': 10, 'GLU:plan': 8, 'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.14, per 1000 atoms: 0.23 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 - 3.00 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: 0.56 Conformation dependent library (CDL) restraints added in 347.3 milliseconds 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... Secondary structure from input PDB file: 61 helices and 4 sheets defined 52.0% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 44 through 48 removed outlier: 3.808A pdb=" N VAL A 47 " --> pdb=" O ASN A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 72 through 86 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 93 through 97 Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 148 through 156 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 160 through 176 removed outlier: 4.192A pdb=" N VAL A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 254 Processing helix chain 'A' and resid 258 through 269 Processing helix chain 'A' and resid 331 through 337 removed outlier: 3.582A pdb=" N TYR A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 387 through 400 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 400 through 418 removed outlier: 3.673A pdb=" N LEU A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) 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 422 through 426 Processing helix chain 'A' and resid 454 through 463 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 468 through 481 removed outlier: 3.552A pdb=" N LEU A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 531 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 539 through 558 removed outlier: 4.321A pdb=" N VAL A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 Processing helix chain 'A' and resid 592 through 596 Processing helix chain 'A' and resid 605 through 617 removed outlier: 3.587A pdb=" N MET A 609 " --> pdb=" O PRO A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 635 removed outlier: 3.812A pdb=" N VAL A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 655 through 663 Processing helix chain 'A' and resid 695 through 701 removed outlier: 4.028A pdb=" N GLY A 699 " --> pdb=" O ASP A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 712 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 716 through 733 removed outlier: 3.749A pdb=" N PHE A 720 " --> pdb=" O ALA A 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 71 removed outlier: 4.651A pdb=" N VAL B 68 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA B 69 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 71 " --> pdb=" O VAL B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 84 removed outlier: 3.662A pdb=" N GLU B 82 " --> pdb=" O ARG B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 98 through 111 Processing helix chain 'B' and resid 125 through 129 removed outlier: 3.591A pdb=" N ARG B 128 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 148 removed outlier: 3.968A pdb=" N LEU B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 156 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 160 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 240 through 254 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 258 through 270 removed outlier: 3.577A pdb=" N HIS B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 330 through 337 removed outlier: 3.987A pdb=" N GLU B 334 " --> pdb=" O ASN B 330 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 383 Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 387 through 400 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 400 through 417 removed outlier: 4.155A pdb=" N LEU B 404 " --> pdb=" O HIS B 400 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 436 through 440 Processing helix chain 'B' and resid 454 through 464 removed outlier: 3.506A pdb=" N LEU B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 482 removed outlier: 4.201A pdb=" N SER B 482 " --> pdb=" O ALA B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 498 removed outlier: 3.800A pdb=" N ARG B 498 " --> pdb=" O GLY B 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 499 through 504 Processing helix chain 'B' and resid 513 through 531 removed outlier: 3.578A pdb=" N VAL B 517 " --> pdb=" O ASP B 513 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG B 519 " --> pdb=" O ARG B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 560 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 575 through 579 Processing helix chain 'B' and resid 580 through 585 removed outlier: 3.642A pdb=" N ALA B 585 " --> pdb=" O VAL B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 596 removed outlier: 3.717A pdb=" N ASN B 596 " --> pdb=" O GLY B 593 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 593 through 596' Processing helix chain 'B' and resid 605 through 617 Processing helix chain 'B' and resid 620 through 635 removed outlier: 3.659A pdb=" N VAL B 633 " --> pdb=" O GLY B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 655 through 662 Processing helix chain 'B' and resid 696 through 700 Processing helix chain 'B' and resid 704 through 712 removed outlier: 3.758A pdb=" N VAL B 708 " --> pdb=" O LEU B 704 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 710 " --> pdb=" O ALA B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 733 removed outlier: 3.557A pdb=" N PHE B 720 " --> pdb=" O ALA B 716 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 667 through 670 removed outlier: 3.568A pdb=" N TRP A 689 " --> pdb=" O GLY A 680 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 342 through 344 Processing sheet with id=AA3, first strand: chain 'B' and resid 591 through 592 Processing sheet with id=AA4, 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) 365 hydrogen bonds defined for protein. 993 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 0.78 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: 0.00 - 1.73: 12530 1.73 - 3.46: 292 3.46 - 5.18: 34 5.18 - 6.91: 7 6.91 - 8.64: 1 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: 1824 2.77 - 3.30: 8970 3.30 - 3.83: 14258 3.83 - 4.37: 16753 4.37 - 4.90: 29179 Nonbonded interactions: 70984 Sorted by model distance: nonbonded pdb=" O MET B 420 " pdb=" NH1 ARG B 425 " model vdw 2.232 3.120 nonbonded pdb=" OE2 GLU B 506 " pdb=" OH TYR B 638 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR A 337 " pdb=" OG1 THR A 394 " model vdw 2.291 3.040 nonbonded pdb=" OD1 ASP A 406 " pdb=" NZ LYS A 410 " model vdw 2.294 3.120 nonbonded pdb=" OE1 GLN A 88 " pdb=" NE1 TRP A 90 " model vdw 2.295 3.120 ... (remaining 70979 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' 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 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 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: 1.290 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.530 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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= 0.178 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 : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 496 TYR 0.011 0.001 TYR A 638 PHE 0.012 0.001 PHE B 167 TRP 0.013 0.001 TRP A 728 HIS 0.002 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 9435) covalent geometry : angle 0.61753 (12864) hydrogen bonds : bond 0.19241 ( 365) hydrogen bonds : angle 6.36726 ( 993) *********************** 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 to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 732 MET cc_start: 0.8831 (mmt) cc_final: 0.8624 (mmt) REVERT: B 262 THR cc_start: 0.8631 (m) cc_final: 0.8367 (m) REVERT: B 420 MET cc_start: 0.8636 (ttt) cc_final: 0.8398 (ttt) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0838 time to fit residues: 5.7852 Evaluate side-chains 39 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 0.0070 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.117757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.091849 restraints weight = 19922.221| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 3.38 r_work: 0.3401 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9435 Z= 0.100 Angle : 0.511 6.272 12864 Z= 0.255 Chirality : 0.039 0.132 1387 Planarity : 0.004 0.044 1680 Dihedral : 4.628 64.548 1310 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.11 % Allowed : 3.16 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.25), residues: 1197 helix: 0.10 (0.24), residues: 522 sheet: -3.72 (1.09), residues: 22 loop : -2.00 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 489 TYR 0.017 0.001 TYR A 638 PHE 0.009 0.001 PHE B 584 TRP 0.012 0.001 TRP A 728 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 9435) covalent geometry : angle 0.51084 (12864) hydrogen bonds : bond 0.03422 ( 365) hydrogen bonds : angle 4.34052 ( 993) *********************** 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 to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.226 Fit side-chains REVERT: A 176 MET cc_start: 0.8737 (mmm) cc_final: 0.8409 (mmt) REVERT: A 242 MET cc_start: 0.8068 (mpp) cc_final: 0.7789 (mpp) REVERT: B 84 MET cc_start: 0.8739 (ptp) cc_final: 0.8538 (mtm) outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.1025 time to fit residues: 6.7487 Evaluate side-chains 42 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 97 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 63 optimal weight: 7.9990 chunk 120 optimal weight: 0.7980 chunk 19 optimal weight: 0.0970 chunk 52 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 596 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.118288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.092727 restraints weight = 19928.140| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 3.37 r_work: 0.3414 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9435 Z= 0.091 Angle : 0.478 6.336 12864 Z= 0.235 Chirality : 0.038 0.134 1387 Planarity : 0.004 0.046 1680 Dihedral : 4.421 65.185 1310 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.45 % Allowed : 4.96 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.25), residues: 1197 helix: 0.38 (0.24), residues: 528 sheet: -3.61 (1.09), residues: 22 loop : -1.83 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 632 TYR 0.013 0.001 TYR A 638 PHE 0.007 0.001 PHE B 167 TRP 0.010 0.001 TRP A 728 HIS 0.002 0.000 HIS B 561 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 9435) covalent geometry : angle 0.47770 (12864) hydrogen bonds : bond 0.03114 ( 365) hydrogen bonds : angle 3.94858 ( 993) *********************** 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 50 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.348 Fit side-chains REVERT: A 91 TRP cc_start: 0.7960 (t-100) cc_final: 0.7615 (t-100) REVERT: A 176 MET cc_start: 0.8729 (mmm) cc_final: 0.8363 (mmt) REVERT: A 242 MET cc_start: 0.7937 (mpp) cc_final: 0.7680 (mpp) outliers start: 4 outliers final: 1 residues processed: 47 average time/residue: 0.0785 time to fit residues: 5.8321 Evaluate side-chains 43 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 109 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 86 optimal weight: 0.3980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.117206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.091461 restraints weight = 20292.588| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.41 r_work: 0.3252 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1251 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= 0.111 Angle : 0.484 8.040 12864 Z= 0.235 Chirality : 0.038 0.134 1387 Planarity : 0.004 0.046 1680 Dihedral : 4.392 65.981 1310 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.23 % Allowed : 6.54 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.25), residues: 1197 helix: 0.61 (0.24), residues: 527 sheet: -3.50 (1.08), residues: 22 loop : -1.73 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 498 TYR 0.005 0.001 TYR B 98 PHE 0.009 0.001 PHE B 167 TRP 0.008 0.001 TRP A 728 HIS 0.003 0.000 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9435) covalent geometry : angle 0.48372 (12864) hydrogen bonds : bond 0.03034 ( 365) hydrogen bonds : angle 3.76524 ( 993) *********************** 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 44 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.263 Fit side-chains REVERT: A 91 TRP cc_start: 0.7848 (t-100) cc_final: 0.7534 (t-100) REVERT: A 176 MET cc_start: 0.8803 (mmm) cc_final: 0.8414 (mmt) REVERT: A 242 MET cc_start: 0.7979 (mpp) cc_final: 0.7748 (mpp) outliers start: 2 outliers final: 1 residues processed: 43 average time/residue: 0.0820 time to fit residues: 5.5453 Evaluate side-chains 42 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 76 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 20.0000 chunk 74 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.116684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.090795 restraints weight = 20246.640| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.41 r_work: 0.3242 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9435 Z= 0.122 Angle : 0.484 7.193 12864 Z= 0.236 Chirality : 0.039 0.135 1387 Planarity : 0.004 0.045 1680 Dihedral : 4.408 66.056 1310 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.56 % Allowed : 6.99 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.25), residues: 1197 helix: 0.75 (0.24), residues: 530 sheet: -3.49 (0.91), residues: 27 loop : -1.63 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 498 TYR 0.005 0.001 TYR A 413 PHE 0.009 0.001 PHE B 167 TRP 0.008 0.001 TRP A 728 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9435) covalent geometry : angle 0.48385 (12864) hydrogen bonds : bond 0.03017 ( 365) hydrogen bonds : angle 3.68749 ( 993) *********************** 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 49 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.343 Fit side-chains REVERT: A 176 MET cc_start: 0.8802 (mmm) cc_final: 0.8398 (mmt) REVERT: A 242 MET cc_start: 0.8001 (mpp) cc_final: 0.7784 (mpp) outliers start: 5 outliers final: 3 residues processed: 47 average time/residue: 0.0836 time to fit residues: 5.9918 Evaluate side-chains 44 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 48 optimal weight: 0.8980 chunk 1 optimal weight: 0.0170 chunk 118 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 114 optimal weight: 0.0670 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.118772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.092954 restraints weight = 20054.833| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.42 r_work: 0.3421 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9435 Z= 0.086 Angle : 0.462 7.784 12864 Z= 0.223 Chirality : 0.038 0.134 1387 Planarity : 0.004 0.045 1680 Dihedral : 4.194 65.281 1310 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.34 % Allowed : 7.78 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.25), residues: 1197 helix: 1.00 (0.24), residues: 529 sheet: -5.12 (0.89), residues: 10 loop : -1.58 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 640 TYR 0.005 0.001 TYR B 155 PHE 0.007 0.001 PHE B 167 TRP 0.012 0.001 TRP A 91 HIS 0.003 0.000 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 9435) covalent geometry : angle 0.46198 (12864) hydrogen bonds : bond 0.02561 ( 365) hydrogen bonds : angle 3.48949 ( 993) *********************** 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 50 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.335 Fit side-chains REVERT: A 91 TRP cc_start: 0.7929 (t-100) cc_final: 0.7518 (t-100) REVERT: A 176 MET cc_start: 0.8684 (mmm) cc_final: 0.8321 (mmt) outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 0.0726 time to fit residues: 5.6713 Evaluate side-chains 48 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 104 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 94 optimal weight: 0.0010 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.2980 chunk 114 optimal weight: 2.9990 overall best weight: 1.2190 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.117045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.090675 restraints weight = 20251.998| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 3.43 r_work: 0.3397 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1526 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= 0.115 Angle : 0.490 10.534 12864 Z= 0.235 Chirality : 0.039 0.135 1387 Planarity : 0.004 0.044 1680 Dihedral : 4.293 66.494 1310 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.68 % Allowed : 8.46 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.25), residues: 1197 helix: 1.04 (0.24), residues: 530 sheet: -4.20 (0.99), residues: 15 loop : -1.52 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 640 TYR 0.015 0.001 TYR A 95 PHE 0.009 0.001 PHE B 167 TRP 0.009 0.001 TRP A 91 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9435) covalent geometry : angle 0.48963 (12864) hydrogen bonds : bond 0.02835 ( 365) hydrogen bonds : angle 3.50009 ( 993) *********************** 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 49 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.241 Fit side-chains REVERT: A 91 TRP cc_start: 0.7973 (t-100) cc_final: 0.7567 (t-100) REVERT: A 176 MET cc_start: 0.8673 (mmm) cc_final: 0.8311 (mmt) outliers start: 6 outliers final: 5 residues processed: 48 average time/residue: 0.0732 time to fit residues: 5.4967 Evaluate side-chains 47 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 96 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.117361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.090964 restraints weight = 20096.475| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.42 r_work: 0.3399 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9435 Z= 0.108 Angle : 0.485 11.416 12864 Z= 0.232 Chirality : 0.038 0.137 1387 Planarity : 0.004 0.043 1680 Dihedral : 4.265 66.016 1310 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.79 % Allowed : 8.79 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.25), residues: 1197 helix: 1.10 (0.24), residues: 530 sheet: -4.11 (1.03), residues: 15 loop : -1.48 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 640 TYR 0.013 0.001 TYR A 95 PHE 0.009 0.001 PHE B 167 TRP 0.009 0.001 TRP A 91 HIS 0.003 0.000 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9435) covalent geometry : angle 0.48489 (12864) hydrogen bonds : bond 0.02761 ( 365) hydrogen bonds : angle 3.47083 ( 993) *********************** 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 50 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.317 Fit side-chains REVERT: A 91 TRP cc_start: 0.7951 (t-100) cc_final: 0.7539 (t-100) REVERT: A 176 MET cc_start: 0.8661 (mmm) cc_final: 0.8293 (mmt) REVERT: B 732 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8643 (mmm) outliers start: 7 outliers final: 4 residues processed: 47 average time/residue: 0.0770 time to fit residues: 5.7868 Evaluate side-chains 47 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 72 optimal weight: 0.0980 chunk 48 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.118447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.092229 restraints weight = 19968.940| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.41 r_work: 0.3422 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9435 Z= 0.089 Angle : 0.479 13.308 12864 Z= 0.227 Chirality : 0.038 0.135 1387 Planarity : 0.003 0.043 1680 Dihedral : 4.156 65.667 1310 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.68 % Allowed : 9.02 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.25), residues: 1197 helix: 1.27 (0.24), residues: 529 sheet: -4.02 (1.06), residues: 15 loop : -1.43 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 187 TYR 0.013 0.001 TYR A 95 PHE 0.008 0.001 PHE B 167 TRP 0.007 0.001 TRP A 91 HIS 0.003 0.000 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 9435) covalent geometry : angle 0.47944 (12864) hydrogen bonds : bond 0.02555 ( 365) hydrogen bonds : angle 3.38483 ( 993) *********************** 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 53 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.343 Fit side-chains REVERT: A 91 TRP cc_start: 0.7897 (t-100) cc_final: 0.7492 (t-100) REVERT: A 176 MET cc_start: 0.8617 (mmm) cc_final: 0.8248 (mmt) outliers start: 6 outliers final: 4 residues processed: 50 average time/residue: 0.0753 time to fit residues: 5.9925 Evaluate side-chains 47 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.118017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.092260 restraints weight = 20080.164| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.40 r_work: 0.3409 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9435 Z= 0.108 Angle : 0.490 11.654 12864 Z= 0.234 Chirality : 0.039 0.156 1387 Planarity : 0.003 0.043 1680 Dihedral : 4.216 66.235 1310 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.68 % Allowed : 9.13 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.25), residues: 1197 helix: 1.32 (0.23), residues: 529 sheet: -3.99 (1.08), residues: 15 loop : -1.40 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 640 TYR 0.012 0.001 TYR A 95 PHE 0.009 0.001 PHE B 167 TRP 0.008 0.001 TRP A 91 HIS 0.002 0.000 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9435) covalent geometry : angle 0.49032 (12864) hydrogen bonds : bond 0.02689 ( 365) hydrogen bonds : angle 3.39832 ( 993) ********************** 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 51 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.343 Fit side-chains REVERT: A 91 TRP cc_start: 0.7905 (t-100) cc_final: 0.7500 (t-100) REVERT: A 176 MET cc_start: 0.8618 (mmm) cc_final: 0.8256 (mmt) outliers start: 6 outliers final: 6 residues processed: 48 average time/residue: 0.0753 time to fit residues: 5.7922 Evaluate side-chains 50 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 7 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 115 optimal weight: 0.0000 chunk 54 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.118519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.092392 restraints weight = 19801.378| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.38 r_work: 0.3429 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9435 Z= 0.090 Angle : 0.476 10.875 12864 Z= 0.227 Chirality : 0.038 0.135 1387 Planarity : 0.003 0.043 1680 Dihedral : 4.132 65.654 1310 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.56 % Allowed : 9.36 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.25), residues: 1197 helix: 1.50 (0.24), residues: 526 sheet: -3.88 (1.09), residues: 15 loop : -1.34 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 640 TYR 0.012 0.001 TYR A 95 PHE 0.009 0.001 PHE B 167 TRP 0.007 0.001 TRP A 91 HIS 0.002 0.000 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 9435) covalent geometry : angle 0.47618 (12864) hydrogen bonds : bond 0.02502 ( 365) hydrogen bonds : angle 3.33865 ( 993) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1652.44 seconds wall clock time: 28 minutes 56.26 seconds (1736.26 seconds total)