Starting phenix.real_space_refine on Fri Oct 23 05:36:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yb0_72744/10_2026/9yb0_72744.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yb0_72744/10_2026/9yb0_72744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yb0_72744/10_2026/9yb0_72744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yb0_72744/10_2026/9yb0_72744.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yb0_72744/10_2026/9yb0_72744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yb0_72744/10_2026/9yb0_72744.map" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 5290 2.51 5 N 1554 2.21 5 O 1631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8485 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 4328 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 471} Link IDs: {'PTRANS': 17, 'TRANS': 723} Chain breaks: 6 Unresolved non-hydrogen bonds: 1803 Unresolved non-hydrogen angles: 2276 Unresolved non-hydrogen dihedrals: 1500 Unresolved non-hydrogen chiralities: 130 Planarities with less than four sites: {'ASN:plan1': 46, 'GLN:plan1': 17, 'PHE:plan': 23, 'ARG:plan': 30, 'ASP:plan': 34, 'GLU:plan': 50, 'TYR:plan': 28, 'HIS:plan': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 1075 Chain: "B" Number of atoms: 4157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 4157 Classifications: {'peptide': 725} Incomplete info: {'truncation_to_alanine': 484} Link IDs: {'PTRANS': 14, 'TRANS': 710} Chain breaks: 6 Unresolved non-hydrogen bonds: 1853 Unresolved non-hydrogen angles: 2335 Unresolved non-hydrogen dihedrals: 1543 Unresolved non-hydrogen chiralities: 135 Planarities with less than four sites: {'ASN:plan1': 45, 'GLU:plan': 52, 'PHE:plan': 24, 'GLN:plan1': 17, 'ARG:plan': 32, 'ASP:plan': 33, 'TYR:plan': 28, 'HIS:plan': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 1093 Time building chain proxies: 2.05, per 1000 atoms: 0.24 Number of scatterers: 8485 At special positions: 0 Unit cell: (96.3, 118.77, 107, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 1631 8.00 N 1554 7.00 C 5290 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: 0.76 Conformation dependent library (CDL) restraints added in 335.9 milliseconds 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2824 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 8 sheets defined 50.8% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 removed outlier: 3.655A pdb=" N LYS A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.641A pdb=" N ALA A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 76 through 86 removed outlier: 3.740A pdb=" N LEU A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 4.560A pdb=" N ILE A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 119 removed outlier: 3.630A pdb=" N LEU A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.776A pdb=" N SER A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 173 Processing helix chain 'A' and resid 183 through 192 removed outlier: 4.527A pdb=" N GLU A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 202 removed outlier: 3.852A pdb=" N PHE A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 242 through 252 removed outlier: 4.165A pdb=" N ALA A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 294 through 299 removed outlier: 3.944A pdb=" N ILE A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 removed outlier: 3.601A pdb=" N GLY A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 340 Processing helix chain 'A' and resid 350 through 364 removed outlier: 3.775A pdb=" N SER A 354 " --> pdb=" O PHE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 388 removed outlier: 3.933A pdb=" N ASN A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 411 removed outlier: 3.636A pdb=" N ASP A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 440 removed outlier: 3.824A pdb=" N LYS A 439 " --> pdb=" O LYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 removed outlier: 4.611A pdb=" N ASP A 462 " --> pdb=" O ASN A 458 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LYS A 463 " --> pdb=" O TYR A 459 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.780A pdb=" N LEU A 493 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 517 removed outlier: 3.977A pdb=" N LEU A 511 " --> pdb=" O SER A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 526 Processing helix chain 'A' and resid 534 through 539 removed outlier: 3.968A pdb=" N ILE A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 577 Processing helix chain 'A' and resid 579 through 594 Processing helix chain 'A' and resid 596 through 603 removed outlier: 4.118A pdb=" N SER A 600 " --> pdb=" O PHE A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 629 removed outlier: 3.568A pdb=" N TYR A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 638 through 644 removed outlier: 4.811A pdb=" N ALA A 644 " --> pdb=" O TRP A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 654 through 668 Processing helix chain 'A' and resid 676 through 694 removed outlier: 3.692A pdb=" N SER A 681 " --> pdb=" O GLN A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 716 Processing helix chain 'A' and resid 735 through 742 removed outlier: 3.837A pdb=" N GLN A 740 " --> pdb=" O ARG A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 767 removed outlier: 4.333A pdb=" N ASN A 758 " --> pdb=" O LYS A 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 21 removed outlier: 3.834A pdb=" N ILE B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 58 Processing helix chain 'B' and resid 64 through 72 removed outlier: 3.816A pdb=" N ILE B 68 " --> pdb=" O THR B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 91 through 102 removed outlier: 4.303A pdb=" N ILE B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 119 removed outlier: 3.658A pdb=" N LEU B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 removed outlier: 3.739A pdb=" N SER B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 183 through 192 removed outlier: 4.592A pdb=" N GLU B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU B 191 " --> pdb=" O HIS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 202 removed outlier: 4.136A pdb=" N PHE B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 226 Processing helix chain 'B' and resid 242 through 252 removed outlier: 4.022A pdb=" N ALA B 248 " --> pdb=" O GLU B 244 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 274 Processing helix chain 'B' and resid 327 through 338 removed outlier: 4.141A pdb=" N ASP B 331 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 362 removed outlier: 3.660A pdb=" N LYS B 353 " --> pdb=" O ARG B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 388 removed outlier: 3.777A pdb=" N LYS B 383 " --> pdb=" O ASP B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 411 removed outlier: 3.775A pdb=" N GLU B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 433 Processing helix chain 'B' and resid 433 through 439 Processing helix chain 'B' and resid 456 through 461 Processing helix chain 'B' and resid 462 through 464 No H-bonds generated for 'chain 'B' and resid 462 through 464' Processing helix chain 'B' and resid 477 through 490 removed outlier: 3.740A pdb=" N PHE B 481 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR B 485 " --> pdb=" O PHE B 481 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR B 486 " --> pdb=" O ALA B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 493 No H-bonds generated for 'chain 'B' and resid 491 through 493' Processing helix chain 'B' and resid 507 through 517 removed outlier: 3.916A pdb=" N LEU B 511 " --> pdb=" O SER B 507 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B 515 " --> pdb=" O LEU B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 526 Processing helix chain 'B' and resid 534 through 539 removed outlier: 3.966A pdb=" N ILE B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 577 Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 596 through 603 removed outlier: 4.073A pdb=" N SER B 600 " --> pdb=" O PHE B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 611 Processing helix chain 'B' and resid 618 through 629 removed outlier: 3.514A pdb=" N ARG B 623 " --> pdb=" O HIS B 619 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 634 Processing helix chain 'B' and resid 654 through 668 Processing helix chain 'B' and resid 676 through 694 removed outlier: 3.860A pdb=" N SER B 681 " --> pdb=" O GLN B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 716 removed outlier: 3.693A pdb=" N LEU B 711 " --> pdb=" O PHE B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 765 removed outlier: 5.344A pdb=" N ILE B 761 " --> pdb=" O VAL B 757 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN B 762 " --> pdb=" O ASN B 758 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 126 removed outlier: 3.726A pdb=" N THR A 126 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LYS A 141 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LYS A 162 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU A 143 " --> pdb=" O LYS A 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 209 through 210 Processing sheet with id=AA3, first strand: chain 'A' and resid 368 through 372 removed outlier: 6.481A pdb=" N ASN A 368 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL A 395 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SER A 370 " --> pdb=" O VAL A 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 520 through 521 removed outlier: 3.684A pdb=" N ALA A 520 " --> pdb=" O ILE A 558 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 24 through 25 removed outlier: 4.292A pdb=" N LEU B 209 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE B 208 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 126 removed outlier: 4.007A pdb=" N THR B 126 " --> pdb=" O PHE B 161 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS B 141 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LYS B 162 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU B 143 " --> pdb=" O LYS B 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 393 through 395 removed outlier: 6.259A pdb=" N PHE B 394 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N CYS B 423 " --> pdb=" O PHE B 394 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU B 344 " --> pdb=" O ILE B 446 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 520 through 521 removed outlier: 3.699A pdb=" N ALA B 520 " --> pdb=" O ILE B 558 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1185 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: 1.29 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3035 1.34 - 1.46: 955 1.46 - 1.57: 4577 1.57 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 8579 Sorted by residual: bond pdb=" N SER B 709 " pdb=" CA SER B 709 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.20e-02 6.94e+03 9.00e+00 bond pdb=" N LYS B 280 " pdb=" CA LYS B 280 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.71e+00 bond pdb=" CA SER B 281 " pdb=" CB SER B 281 " ideal model delta sigma weight residual 1.530 1.485 0.045 2.00e-02 2.50e+03 5.16e+00 bond pdb=" N LEU B 711 " pdb=" CA LEU B 711 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.10e+00 bond pdb=" N SER B 710 " pdb=" CA SER B 710 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.23e-02 6.61e+03 4.41e+00 ... (remaining 8574 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 11614 2.27 - 4.54: 209 4.54 - 6.81: 24 6.81 - 9.08: 4 9.08 - 11.35: 1 Bond angle restraints: 11852 Sorted by residual: angle pdb=" N ASP A 261 " pdb=" CA ASP A 261 " pdb=" C ASP A 261 " ideal model delta sigma weight residual 111.96 117.60 -5.64 1.41e+00 5.03e-01 1.60e+01 angle pdb=" CA SER B 709 " pdb=" C SER B 709 " pdb=" O SER B 709 " ideal model delta sigma weight residual 120.70 116.97 3.73 1.03e+00 9.43e-01 1.31e+01 angle pdb=" CA THR B 283 " pdb=" C THR B 283 " pdb=" O THR B 283 " ideal model delta sigma weight residual 120.80 114.82 5.98 1.70e+00 3.46e-01 1.24e+01 angle pdb=" CA LEU A 288 " pdb=" CB LEU A 288 " pdb=" CG LEU A 288 " ideal model delta sigma weight residual 116.30 127.65 -11.35 3.50e+00 8.16e-02 1.05e+01 angle pdb=" N LYS B 743 " pdb=" CA LYS B 743 " pdb=" C LYS B 743 " ideal model delta sigma weight residual 113.21 109.61 3.60 1.15e+00 7.56e-01 9.82e+00 ... (remaining 11847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.35: 4773 13.35 - 26.69: 210 26.69 - 40.04: 40 40.04 - 53.39: 8 53.39 - 66.74: 3 Dihedral angle restraints: 5034 sinusoidal: 745 harmonic: 4289 Sorted by residual: dihedral pdb=" CA GLN B 447 " pdb=" C GLN B 447 " pdb=" N ILE B 448 " pdb=" CA ILE B 448 " ideal model delta harmonic sigma weight residual 180.00 153.96 26.04 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA SER B 650 " pdb=" C SER B 650 " pdb=" N ALA B 651 " pdb=" CA ALA B 651 " ideal model delta harmonic sigma weight residual 180.00 156.13 23.87 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA TYR B 483 " pdb=" C TYR B 483 " pdb=" N ARG B 484 " pdb=" CA ARG B 484 " ideal model delta harmonic sigma weight residual 180.00 156.15 23.85 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 5031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1063 0.040 - 0.080: 376 0.080 - 0.121: 85 0.121 - 0.161: 13 0.161 - 0.201: 5 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CB ILE B 254 " pdb=" CA ILE B 254 " pdb=" CG1 ILE B 254 " pdb=" CG2 ILE B 254 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE A 254 " pdb=" CA ILE A 254 " pdb=" CG1 ILE A 254 " pdb=" CG2 ILE A 254 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.64e-01 chirality pdb=" CB THR B 64 " pdb=" CA THR B 64 " pdb=" OG1 THR B 64 " pdb=" CG2 THR B 64 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.58e-01 ... (remaining 1539 not shown) Planarity restraints: 1612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 306 " -0.084 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO A 307 " 0.220 5.00e-02 4.00e+02 pdb=" CA PRO A 307 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO A 307 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 708 " -0.024 2.00e-02 2.50e+03 4.76e-02 2.26e+01 pdb=" C GLU B 708 " 0.082 2.00e-02 2.50e+03 pdb=" O GLU B 708 " -0.031 2.00e-02 2.50e+03 pdb=" N SER B 709 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 279 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.84e+00 pdb=" C ARG B 279 " -0.051 2.00e-02 2.50e+03 pdb=" O ARG B 279 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS B 280 " 0.017 2.00e-02 2.50e+03 ... (remaining 1609 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2241 2.79 - 3.32: 8378 3.32 - 3.84: 13278 3.84 - 4.37: 13564 4.37 - 4.90: 22599 Nonbonded interactions: 60060 Sorted by model distance: nonbonded pdb=" O ASN A 697 " pdb=" ND2 ASN A 697 " model vdw 2.261 3.120 nonbonded pdb=" O ASP A 130 " pdb=" NZ LYS A 162 " model vdw 2.262 3.120 nonbonded pdb=" OD1 ASP B 131 " pdb=" N ALA B 132 " model vdw 2.305 3.120 nonbonded pdb=" O PHE A 394 " pdb=" N VAL A 421 " model vdw 2.309 3.120 nonbonded pdb=" O GLY B 82 " pdb=" N MET B 86 " model vdw 2.320 3.120 ... (remaining 60055 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 10 through 21 and (name N or name CA or name C or name O \ or name CB )) or resid 22 through 23 or (resid 24 through 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26 through 33 or (resid 34 throug \ h 38 and (name N or name CA or name C or name O or name CB )) or resid 39 throug \ h 41 or (resid 42 and (name N or name CA or name C or name O or name CB )) or re \ sid 43 through 53 or (resid 54 and (name N or name CA or name C or name O or nam \ e CB )) or resid 55 through 77 or (resid 78 through 81 and (name N or name CA or \ name C or name O or name CB )) or resid 82 through 232 or (resid 233 through 23 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 239 through \ 281 or resid 283 through 295 or (resid 296 through 297 and (name N or name CA or \ name C or name O or name CB )) or resid 317 through 465 or resid 468 through 49 \ 8 or (resid 499 through 522 and (name N or name CA or name C or name O or name C \ B )) or resid 523 through 695 or (resid 696 and (name N or name CA or name C or \ name O or name CB )) or (resid 700 through 708 and (name N or name CA or name C \ or name O or name CB )) or resid 709 through 716 or resid 719 through 767)) selection = (chain 'B' and (resid 10 through 130 or (resid 131 through 132 and (name N or na \ me CA or name C or name O or name CB )) or resid 133 through 423 or resid 427 th \ rough 450 or resid 452 through 476 or resid 478 through 704 or (resid 705 throug \ h 708 and (name N or name CA or name C or name O or name CB )) or resid 709 thro \ ugh 767)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.900 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3853 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8579 Z= 0.163 Angle : 0.726 11.346 11852 Z= 0.411 Chirality : 0.043 0.201 1542 Planarity : 0.006 0.127 1612 Dihedral : 9.401 66.737 2210 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 1.11 % Allowed : 17.04 % Favored : 81.85 % Rotamer: Outliers : 0.80 % Allowed : 0.00 % Favored : 99.20 % 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: -3.78 (0.20), residues: 1438 helix: -1.02 (0.20), residues: 609 sheet: -3.47 (0.63), residues: 49 loop : -3.89 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 34 TYR 0.006 0.001 TYR A 372 PHE 0.018 0.002 PHE A 208 TRP 0.024 0.002 TRP B 269 HIS 0.009 0.002 HIS B 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.16 ( 8579) covalent geometry : angle 0.72591 / 0.41 (11852) hydrogen bonds : bond 0.17426 / 12.26 ( 401) hydrogen bonds : angle 7.76497 / 5.42 ( 1185) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 10 ASN cc_start: 0.6332 (p0) cc_final: 0.5893 (p0) REVERT: A 697 ASN cc_start: 0.4211 (OUTLIER) cc_final: 0.3570 (m-40) REVERT: B 55 ASN cc_start: 0.6685 (m-40) cc_final: 0.6298 (m-40) outliers start: 3 outliers final: 0 residues processed: 100 average time/residue: 0.0602 time to fit residues: 9.3660 Evaluate side-chains 80 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.0570 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.1737 > 50:) chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 HIS A 697 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5132 r_free = 0.5132 target = 0.263262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4993 r_free = 0.4993 target = 0.247558 restraints weight = 18435.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.5019 r_free = 0.5019 target = 0.249981 restraints weight = 13974.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5030 r_free = 0.5030 target = 0.251496 restraints weight = 10592.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5037 r_free = 0.5037 target = 0.252264 restraints weight = 8332.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.5052 r_free = 0.5052 target = 0.254078 restraints weight = 6913.651| |-----------------------------------------------------------------------------| r_work (final): 0.5059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3947 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8579 Z= 0.150 Angle : 0.641 9.263 11852 Z= 0.353 Chirality : 0.042 0.243 1542 Planarity : 0.005 0.091 1612 Dihedral : 5.810 22.965 1473 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.70 % Allowed : 15.09 % Favored : 84.21 % Rotamer: Outliers : 1.86 % Allowed : 9.28 % Favored : 88.86 % 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: -3.41 (0.20), residues: 1438 helix: -0.73 (0.20), residues: 636 sheet: -3.11 (0.62), residues: 50 loop : -3.77 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 138 TYR 0.010 0.001 TYR B 372 PHE 0.023 0.002 PHE A 19 TRP 0.014 0.002 TRP B 269 HIS 0.004 0.001 HIS B 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 ( 8579) covalent geometry : angle 0.64095 / 0.35 (11852) hydrogen bonds : bond 0.03977 / 2.82 ( 401) hydrogen bonds : angle 6.18659 / 4.31 ( 1185) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASN cc_start: 0.6556 (p0) cc_final: 0.6096 (p0) REVERT: A 697 ASN cc_start: 0.3701 (p0) cc_final: 0.2801 (t0) REVERT: B 55 ASN cc_start: 0.6833 (m-40) cc_final: 0.6558 (m110) outliers start: 7 outliers final: 3 residues processed: 82 average time/residue: 0.0630 time to fit residues: 8.0146 Evaluate side-chains 73 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 701 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: [113, 112, 138, 37, 128, 99, 21, 60, 117, 106, 140] chunk 113 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 128 optimal weight: 0.2980 chunk 99 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 117 optimal weight: 0.0570 chunk 106 optimal weight: 0.5980 chunk 140 optimal weight: 0.6980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5116 r_free = 0.5116 target = 0.261847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4971 r_free = 0.4971 target = 0.245605 restraints weight = 18096.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4995 r_free = 0.4995 target = 0.247808 restraints weight = 13733.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4993 r_free = 0.4993 target = 0.247774 restraints weight = 13082.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.5009 r_free = 0.5009 target = 0.249608 restraints weight = 10508.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.5019 r_free = 0.5019 target = 0.250782 restraints weight = 8318.784| |-----------------------------------------------------------------------------| r_work (final): 0.5025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4041 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8579 Z= 0.118 Angle : 0.574 8.292 11852 Z= 0.315 Chirality : 0.040 0.163 1542 Planarity : 0.004 0.071 1612 Dihedral : 5.181 22.302 1471 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.63 % Allowed : 14.26 % Favored : 85.12 % Rotamer: Outliers : 2.39 % Allowed : 12.20 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.21), residues: 1438 helix: -0.45 (0.20), residues: 650 sheet: -2.99 (0.63), residues: 52 loop : -3.68 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 138 TYR 0.011 0.001 TYR B 372 PHE 0.020 0.002 PHE A 19 TRP 0.010 0.001 TRP B 269 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.12 ( 8579) covalent geometry : angle 0.57382 / 0.32 (11852) hydrogen bonds : bond 0.03687 / 2.57 ( 401) hydrogen bonds : angle 5.52859 / 3.83 ( 1185) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.294 Fit side-chains REVERT: A 10 ASN cc_start: 0.6563 (p0) cc_final: 0.6027 (p0) REVERT: A 288 LEU cc_start: 0.3430 (OUTLIER) cc_final: 0.3209 (pp) REVERT: A 697 ASN cc_start: 0.3224 (p0) cc_final: 0.2440 (t0) REVERT: B 55 ASN cc_start: 0.6551 (m-40) cc_final: 0.6273 (m-40) outliers start: 9 outliers final: 5 residues processed: 79 average time/residue: 0.0631 time to fit residues: 7.8615 Evaluate side-chains 73 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 701 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: [101, 43, 48, 115, 8, 26, 33, 141, 72, 126, 89] chunk 101 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 126 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5049 r_free = 0.5049 target = 0.253983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.236974 restraints weight = 17910.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.239218 restraints weight = 13695.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4935 r_free = 0.4935 target = 0.240872 restraints weight = 10631.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4945 r_free = 0.4945 target = 0.241960 restraints weight = 8544.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4950 r_free = 0.4950 target = 0.242541 restraints weight = 7235.318| |-----------------------------------------------------------------------------| r_work (final): 0.4955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4276 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8579 Z= 0.159 Angle : 0.649 9.851 11852 Z= 0.358 Chirality : 0.042 0.231 1542 Planarity : 0.005 0.058 1612 Dihedral : 5.782 21.955 1471 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.63 % Allowed : 16.20 % Favored : 83.17 % Rotamer: Outliers : 2.92 % Allowed : 16.45 % Favored : 80.64 % 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: -3.15 (0.21), residues: 1438 helix: -0.58 (0.20), residues: 647 sheet: -2.91 (0.63), residues: 52 loop : -3.61 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 138 TYR 0.029 0.002 TYR A 267 PHE 0.022 0.002 PHE A 19 TRP 0.010 0.002 TRP B 121 HIS 0.005 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 ( 8579) covalent geometry : angle 0.64929 / 0.36 (11852) hydrogen bonds : bond 0.03924 / 2.75 ( 401) hydrogen bonds : angle 5.99876 / 4.15 ( 1185) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 10 ASN cc_start: 0.6877 (p0) cc_final: 0.6223 (p0) REVERT: A 288 LEU cc_start: 0.3495 (OUTLIER) cc_final: 0.3197 (pp) REVERT: B 55 ASN cc_start: 0.6636 (m-40) cc_final: 0.6413 (m-40) REVERT: B 263 TYR cc_start: 0.1562 (OUTLIER) cc_final: -0.0677 (p90) REVERT: B 394 PHE cc_start: 0.4662 (m-80) cc_final: 0.4173 (m-80) outliers start: 11 outliers final: 6 residues processed: 83 average time/residue: 0.0551 time to fit residues: 7.3297 Evaluate side-chains 78 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 612 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: [125, 48, 41, 126, 8, 16, 26, 7, 12, 20, 10] chunk 125 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.0770 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 697 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5068 r_free = 0.5068 target = 0.256274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.240351 restraints weight = 17825.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.241875 restraints weight = 13910.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4954 r_free = 0.4954 target = 0.243368 restraints weight = 12192.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.244371 restraints weight = 10138.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.245599 restraints weight = 7746.964| |-----------------------------------------------------------------------------| r_work (final): 0.4980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4211 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8579 Z= 0.113 Angle : 0.573 11.136 11852 Z= 0.308 Chirality : 0.039 0.227 1542 Planarity : 0.004 0.057 1612 Dihedral : 5.085 22.980 1471 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.66 % Favored : 86.79 % Rotamer: Outliers : 3.71 % Allowed : 18.57 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.21), residues: 1438 helix: -0.19 (0.20), residues: 653 sheet: -2.74 (0.63), residues: 62 loop : -3.63 (0.20), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 138 TYR 0.011 0.001 TYR A 267 PHE 0.012 0.001 PHE A 170 TRP 0.010 0.001 TRP B 269 HIS 0.002 0.001 HIS B 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 ( 8579) covalent geometry : angle 0.57292 / 0.31 (11852) hydrogen bonds : bond 0.03231 / 2.26 ( 401) hydrogen bonds : angle 5.41851 / 3.75 ( 1185) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 10 ASN cc_start: 0.6805 (p0) cc_final: 0.6146 (p0) REVERT: A 263 TYR cc_start: 0.1933 (OUTLIER) cc_final: 0.0094 (p90) REVERT: B 140 TYR cc_start: 0.5779 (t80) cc_final: 0.3405 (m-80) REVERT: B 394 PHE cc_start: 0.4733 (m-80) cc_final: 0.4231 (m-80) outliers start: 14 outliers final: 7 residues processed: 81 average time/residue: 0.0602 time to fit residues: 7.7896 Evaluate side-chains 74 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 697 ASN Chi-restraints excluded: chain B residue 612 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: [2, 45, 63, 114, 94, 24, 117, 100, 110, 120, 138] chunk 2 optimal weight: 0.0170 chunk 45 optimal weight: 0.0770 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 117 optimal weight: 0.0060 chunk 100 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5067 r_free = 0.5067 target = 0.256345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4941 r_free = 0.4941 target = 0.242120 restraints weight = 17508.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.243336 restraints weight = 13203.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4961 r_free = 0.4961 target = 0.244344 restraints weight = 11304.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4971 r_free = 0.4971 target = 0.245354 restraints weight = 9317.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.246820 restraints weight = 7176.109| |-----------------------------------------------------------------------------| r_work (final): 0.4991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4174 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8579 Z= 0.107 Angle : 0.575 13.993 11852 Z= 0.301 Chirality : 0.039 0.213 1542 Planarity : 0.004 0.050 1612 Dihedral : 4.796 22.723 1471 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.56 % Allowed : 13.63 % Favored : 85.81 % Rotamer: Outliers : 3.18 % Allowed : 19.89 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.22), residues: 1438 helix: 0.06 (0.21), residues: 654 sheet: -2.60 (0.66), residues: 62 loop : -3.60 (0.20), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 54 TYR 0.010 0.001 TYR A 267 PHE 0.012 0.001 PHE A 170 TRP 0.015 0.001 TRP A 269 HIS 0.005 0.001 HIS B 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.11 ( 8579) covalent geometry : angle 0.57509 / 0.30 (11852) hydrogen bonds : bond 0.02937 / 2.06 ( 401) hydrogen bonds : angle 5.24363 / 3.63 ( 1185) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASN cc_start: 0.6927 (p0) cc_final: 0.6246 (p0) REVERT: A 263 TYR cc_start: 0.1681 (OUTLIER) cc_final: -0.0065 (p90) REVERT: B 140 TYR cc_start: 0.5819 (t80) cc_final: 0.3670 (m-80) REVERT: B 263 TYR cc_start: 0.1397 (OUTLIER) cc_final: -0.0781 (p90) REVERT: B 394 PHE cc_start: 0.4732 (m-80) cc_final: 0.4168 (m-80) outliers start: 12 outliers final: 6 residues processed: 75 average time/residue: 0.0532 time to fit residues: 6.5553 Evaluate side-chains 73 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 612 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: [136, 48, 101, 85, 141, 128, 84, 123, 66, 112, 41] chunk 136 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 101 optimal weight: 0.0970 chunk 85 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 697 ASN B 128 ASN B 392 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5024 r_free = 0.5024 target = 0.251261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.234973 restraints weight = 17611.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.236880 restraints weight = 13866.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.237875 restraints weight = 11641.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.239221 restraints weight = 9727.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.240677 restraints weight = 7839.490| |-----------------------------------------------------------------------------| r_work (final): 0.4933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4336 moved from start: 0.5938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8579 Z= 0.135 Angle : 0.613 13.250 11852 Z= 0.329 Chirality : 0.040 0.184 1542 Planarity : 0.004 0.049 1612 Dihedral : 5.171 24.335 1471 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.56 % Allowed : 14.88 % Favored : 84.56 % Rotamer: Outliers : 4.77 % Allowed : 18.83 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.21), residues: 1438 helix: -0.14 (0.20), residues: 655 sheet: -2.65 (0.64), residues: 62 loop : -3.61 (0.20), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 54 TYR 0.020 0.001 TYR A 267 PHE 0.016 0.002 PHE B 532 TRP 0.012 0.001 TRP A 269 HIS 0.004 0.001 HIS B 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 ( 8579) covalent geometry : angle 0.61290 / 0.33 (11852) hydrogen bonds : bond 0.03455 / 2.43 ( 401) hydrogen bonds : angle 5.58257 / 3.88 ( 1185) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 10 ASN cc_start: 0.7014 (p0) cc_final: 0.6673 (p0) REVERT: A 263 TYR cc_start: 0.1815 (OUTLIER) cc_final: 0.0041 (p90) REVERT: B 263 TYR cc_start: 0.1831 (OUTLIER) cc_final: -0.0453 (p90) REVERT: B 394 PHE cc_start: 0.4830 (m-80) cc_final: 0.4216 (m-80) outliers start: 18 outliers final: 9 residues processed: 84 average time/residue: 0.0555 time to fit residues: 7.6232 Evaluate side-chains 78 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 697 ASN Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 612 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: [107, 28, 134, 65, 144, 24, 93, 141, 79, 50, 44] chunk 107 optimal weight: 0.5980 chunk 28 optimal weight: 0.0050 chunk 134 optimal weight: 0.2980 chunk 65 optimal weight: 0.7980 chunk 144 optimal weight: 0.0470 chunk 24 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 44 optimal weight: 0.0670 overall best weight: 0.1030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 392 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5069 r_free = 0.5069 target = 0.256586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4941 r_free = 0.4941 target = 0.241762 restraints weight = 17526.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4949 r_free = 0.4949 target = 0.243323 restraints weight = 16087.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4970 r_free = 0.4970 target = 0.245438 restraints weight = 11598.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4972 r_free = 0.4972 target = 0.245722 restraints weight = 9967.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4986 r_free = 0.4986 target = 0.247309 restraints weight = 7808.632| |-----------------------------------------------------------------------------| r_work (final): 0.4995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4153 moved from start: 0.6089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 8579 Z= 0.094 Angle : 0.574 15.675 11852 Z= 0.297 Chirality : 0.039 0.191 1542 Planarity : 0.004 0.048 1612 Dihedral : 4.492 24.390 1471 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.56 % Allowed : 10.99 % Favored : 88.46 % Rotamer: Outliers : 1.59 % Allowed : 22.81 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.22), residues: 1438 helix: 0.38 (0.21), residues: 660 sheet: -2.54 (0.76), residues: 49 loop : -3.44 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 138 TYR 0.006 0.000 TYR B 263 PHE 0.012 0.001 PHE A 170 TRP 0.011 0.001 TRP B 269 HIS 0.007 0.001 HIS B 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00183 / 0.09 ( 8579) covalent geometry : angle 0.57409 / 0.30 (11852) hydrogen bonds : bond 0.02728 / 1.93 ( 401) hydrogen bonds : angle 4.94728 / 3.42 ( 1185) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 10 ASN cc_start: 0.6748 (p0) cc_final: 0.6071 (p0) REVERT: A 263 TYR cc_start: 0.1677 (OUTLIER) cc_final: -0.0155 (p90) REVERT: B 138 ARG cc_start: 0.7556 (ttp80) cc_final: 0.7340 (ttp80) REVERT: B 394 PHE cc_start: 0.4725 (m-80) cc_final: 0.4072 (m-80) REVERT: B 612 LEU cc_start: 0.3299 (OUTLIER) cc_final: 0.3061 (pp) outliers start: 6 outliers final: 3 residues processed: 78 average time/residue: 0.0607 time to fit residues: 7.5675 Evaluate side-chains 74 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 612 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: [89, 11, 109, 65, 33, 44, 99, 121, 46, 69, 58] chunk 89 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 0.0570 chunk 99 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5010 r_free = 0.5010 target = 0.249406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.232882 restraints weight = 17400.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.235957 restraints weight = 13622.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.235865 restraints weight = 11372.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.237571 restraints weight = 9744.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.239358 restraints weight = 7703.410| |-----------------------------------------------------------------------------| r_work (final): 0.4923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4377 moved from start: 0.6547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8579 Z= 0.157 Angle : 0.647 14.743 11852 Z= 0.342 Chirality : 0.040 0.147 1542 Planarity : 0.004 0.046 1612 Dihedral : 5.173 23.858 1471 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.56 % Allowed : 15.30 % Favored : 84.14 % Rotamer: Outliers : 2.39 % Allowed : 22.81 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.22), residues: 1438 helix: 0.01 (0.21), residues: 652 sheet: -2.71 (0.63), residues: 58 loop : -3.52 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 34 TYR 0.013 0.001 TYR B 267 PHE 0.015 0.002 PHE A 19 TRP 0.015 0.002 TRP A 269 HIS 0.004 0.001 HIS B 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 ( 8579) covalent geometry : angle 0.64709 / 0.34 (11852) hydrogen bonds : bond 0.03579 / 2.51 ( 401) hydrogen bonds : angle 5.57943 / 3.87 ( 1185) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 10 ASN cc_start: 0.6807 (p0) cc_final: 0.6459 (p0) REVERT: A 263 TYR cc_start: 0.1661 (OUTLIER) cc_final: -0.0041 (p90) REVERT: B 263 TYR cc_start: 0.1828 (OUTLIER) cc_final: -0.0504 (p90) REVERT: B 394 PHE cc_start: 0.4755 (m-80) cc_final: 0.4083 (m-80) REVERT: B 612 LEU cc_start: 0.3709 (OUTLIER) cc_final: 0.3450 (pp) outliers start: 9 outliers final: 5 residues processed: 76 average time/residue: 0.0539 time to fit residues: 6.7503 Evaluate side-chains 77 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 612 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: [108, 49, 81, 89, 88, 62, 142, 79, 98, 29, 47] chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 81 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 chunk 88 optimal weight: 0.0070 chunk 62 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 79 optimal weight: 0.1980 chunk 98 optimal weight: 1.9990 chunk 29 optimal weight: 0.0770 chunk 47 optimal weight: 1.9990 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 697 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5043 r_free = 0.5043 target = 0.253333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.238032 restraints weight = 17261.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.240025 restraints weight = 13977.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.241568 restraints weight = 10828.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4945 r_free = 0.4945 target = 0.242417 restraints weight = 8590.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4954 r_free = 0.4954 target = 0.243316 restraints weight = 7325.759| |-----------------------------------------------------------------------------| r_work (final): 0.4958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4273 moved from start: 0.6744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8579 Z= 0.100 Angle : 0.587 16.205 11852 Z= 0.304 Chirality : 0.039 0.150 1542 Planarity : 0.004 0.048 1612 Dihedral : 4.580 23.881 1471 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.54 % Favored : 87.97 % Rotamer: Outliers : 2.39 % Allowed : 23.08 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.22), residues: 1438 helix: 0.42 (0.21), residues: 654 sheet: -2.39 (0.74), residues: 51 loop : -3.41 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 138 TYR 0.008 0.001 TYR A 263 PHE 0.017 0.001 PHE B 28 TRP 0.015 0.001 TRP A 269 HIS 0.003 0.001 HIS B 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.10 ( 8579) covalent geometry : angle 0.58699 / 0.30 (11852) hydrogen bonds : bond 0.02833 / 1.99 ( 401) hydrogen bonds : angle 5.04291 / 3.49 ( 1185) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 263 TYR cc_start: 0.1652 (OUTLIER) cc_final: -0.0128 (p90) REVERT: B 138 ARG cc_start: 0.7534 (ttp80) cc_final: 0.7334 (ttp80) REVERT: B 263 TYR cc_start: 0.1753 (OUTLIER) cc_final: -0.0422 (p90) REVERT: B 612 LEU cc_start: 0.3622 (OUTLIER) cc_final: 0.3404 (pp) outliers start: 9 outliers final: 4 residues processed: 75 average time/residue: 0.0604 time to fit residues: 7.0979 Evaluate side-chains 75 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 697 ASN Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 612 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: [92, 110, 73, 72, 40, 126, 105, 53, 38, 56, 91] chunk 92 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 126 optimal weight: 0.4980 chunk 105 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 38 optimal weight: 0.0970 chunk 56 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 697 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5033 r_free = 0.5033 target = 0.251995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.240513 restraints weight = 17244.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.238646 restraints weight = 13062.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.239741 restraints weight = 11433.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.240667 restraints weight = 9233.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.241407 restraints weight = 7681.948| |-----------------------------------------------------------------------------| r_work (final): 0.4942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4318 moved from start: 0.6951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8579 Z= 0.109 Angle : 0.600 16.124 11852 Z= 0.312 Chirality : 0.039 0.146 1542 Planarity : 0.004 0.048 1612 Dihedral : 4.635 23.998 1471 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.42 % Allowed : 13.42 % Favored : 86.16 % Rotamer: Outliers : 2.92 % Allowed : 23.34 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.22), residues: 1438 helix: 0.44 (0.21), residues: 660 sheet: -2.53 (0.67), residues: 58 loop : -3.43 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 151 TYR 0.010 0.001 TYR A 267 PHE 0.011 0.001 PHE B 208 TRP 0.019 0.001 TRP A 269 HIS 0.002 0.001 HIS B 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 ( 8579) covalent geometry : angle 0.59954 / 0.31 (11852) hydrogen bonds : bond 0.02940 / 2.03 ( 401) hydrogen bonds : angle 5.06819 / 3.49 ( 1185) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1352.25 seconds wall clock time: 23 minutes 44.68 seconds (1424.68 seconds total)