Starting phenix.real_space_refine on Wed Mar 4 00:07:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n88_24233/03_2026/7n88_24233.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n88_24233/03_2026/7n88_24233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n88_24233/03_2026/7n88_24233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n88_24233/03_2026/7n88_24233.map" model { file = "/net/cci-nas-00/data/ceres_data/7n88_24233/03_2026/7n88_24233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n88_24233/03_2026/7n88_24233.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 2 7.16 5 S 44 5.16 5 C 5889 2.51 5 N 1650 2.21 5 O 1817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 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: 9402 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4164 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 17, 'TRANS': 514} Chain breaks: 4 Chain: "B" Number of atoms: 5228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5228 Classifications: {'peptide': 688} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 652} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 76 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 6, 'ASP:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 10 Unusual residues: {' FE': 2, 'BCT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.38, per 1000 atoms: 0.25 Number of scatterers: 9402 At special positions: 0 Unit cell: (92.88, 117.72, 141.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 2 26.01 S 44 16.00 O 1817 8.00 N 1650 7.00 C 5889 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 419 " distance=2.06 Simple disulfide: pdb=" SG CYS B 10 " - pdb=" SG CYS B 46 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 37 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS B 158 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 171 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 381 " distance=2.02 Simple disulfide: pdb=" SG CYS B 359 " - pdb=" SG CYS B 372 " distance=2.02 Simple disulfide: pdb=" SG CYS B 406 " - pdb=" SG CYS B 687 " distance=2.01 Simple disulfide: pdb=" SG CYS B 428 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 460 " - pdb=" SG CYS B 535 " distance=2.03 Simple disulfide: pdb=" SG CYS B 484 " - pdb=" SG CYS B 678 " distance=2.03 Simple disulfide: pdb=" SG CYS B 494 " - pdb=" SG CYS B 508 " distance=2.03 Simple disulfide: pdb=" SG CYS B 505 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 576 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 628 " - pdb=" SG CYS B 633 " distance=2.04 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: 0.78 Conformation dependent library (CDL) restraints added in 533.7 milliseconds 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2222 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 21.5% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 91 through 107 Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.679A pdb=" N ASN A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 565 through 570 removed outlier: 3.798A pdb=" N ASP A 569 " --> pdb=" O ASN A 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 17 Processing helix chain 'B' and resid 20 through 29 removed outlier: 3.607A pdb=" N GLN B 24 " --> pdb=" O CYS B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 52 removed outlier: 3.859A pdb=" N CYS B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 70 removed outlier: 3.536A pdb=" N LEU B 70 " --> pdb=" O TYR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 138 Proline residue: B 135 - end of helix removed outlier: 3.962A pdb=" N ASN B 138 " --> pdb=" O ARG B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 4.157A pdb=" N CYS B 171 " --> pdb=" O PRO B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 182 removed outlier: 4.345A pdb=" N CYS B 182 " --> pdb=" O GLU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 202 removed outlier: 4.834A pdb=" N LEU B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 246 removed outlier: 3.620A pdb=" N LYS B 242 " --> pdb=" O PRO B 239 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LYS B 244 " --> pdb=" O ASP B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 279 removed outlier: 3.547A pdb=" N ILE B 268 " --> pdb=" O LYS B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 321 Processing helix chain 'B' and resid 323 through 331 Processing helix chain 'B' and resid 352 through 366 Processing helix chain 'B' and resid 377 through 388 removed outlier: 4.147A pdb=" N LYS B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 405 Processing helix chain 'B' and resid 427 through 431 removed outlier: 4.034A pdb=" N ARG B 431 " --> pdb=" O CYS B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 455 removed outlier: 3.628A pdb=" N VAL B 454 " --> pdb=" O TRP B 451 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS B 455 " --> pdb=" O ASN B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 482 Processing helix chain 'B' and resid 528 through 538 removed outlier: 3.774A pdb=" N ALA B 537 " --> pdb=" O PHE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 553 removed outlier: 3.676A pdb=" N LEU B 552 " --> pdb=" O ASP B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 583 through 587 removed outlier: 3.583A pdb=" N GLU B 586 " --> pdb=" O PRO B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 617 removed outlier: 3.905A pdb=" N GLN B 617 " --> pdb=" O LEU B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 663 Processing helix chain 'B' and resid 664 through 676 removed outlier: 4.318A pdb=" N TYR B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 690 removed outlier: 3.727A pdb=" N GLU B 685 " --> pdb=" O SER B 681 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA B 686 " --> pdb=" O PRO B 682 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 140 through 143 removed outlier: 6.367A pdb=" N GLU A 140 " --> pdb=" O HIS A 152 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS A 152 " --> pdb=" O GLU A 140 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLU A 142 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 187 removed outlier: 6.718A pdb=" N LEU A 242 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR A 268 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY A 244 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN A 266 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU A 246 " --> pdb=" O ILE A 264 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 377 through 379 removed outlier: 5.569A pdb=" N LEU A 530 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 401 through 406 Processing sheet with id=AA6, first strand: chain 'A' and resid 554 through 557 removed outlier: 5.464A pdb=" N VAL A 696 " --> pdb=" O ILE A 658 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 604 through 605 removed outlier: 3.595A pdb=" N ILE A 585 " --> pdb=" O GLY A 604 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A 584 " --> pdb=" O ASP A 579 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASP A 579 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N HIS A 549 " --> pdb=" O ASP A 703 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL A 696 " --> pdb=" O ILE A 658 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 255 through 258 removed outlier: 6.894A pdb=" N VAL B 256 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 208 through 211 removed outlier: 4.165A pdb=" N ALA B 97 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B 230 " --> pdb=" O LYS B 238 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS B 238 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 115 through 116 removed outlier: 6.540A pdb=" N SER B 115 " --> pdb=" O CYS B 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 393 through 396 removed outlier: 3.508A pdb=" N LEU B 412 " --> pdb=" O VAL B 600 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N SER B 602 " --> pdb=" O PRO B 410 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 544 through 547 Processing sheet with id=AB4, first strand: chain 'B' and resid 544 through 547 260 hydrogen bonds defined for protein. 672 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: 1.20 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3175 1.35 - 1.48: 2345 1.48 - 1.60: 4018 1.60 - 1.73: 0 1.73 - 1.86: 54 Bond restraints: 9592 Sorted by residual: bond pdb=" C BCT B 703 " pdb=" O3 BCT B 703 " ideal model delta sigma weight residual 1.389 1.292 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C BCT B 704 " pdb=" O3 BCT B 704 " ideal model delta sigma weight residual 1.389 1.297 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C VAL B 519 " pdb=" N PRO B 520 " ideal model delta sigma weight residual 1.334 1.301 0.032 8.40e-03 1.42e+04 1.48e+01 bond pdb=" CA LEU A 54 " pdb=" CB LEU A 54 " ideal model delta sigma weight residual 1.528 1.438 0.090 2.61e-02 1.47e+03 1.19e+01 bond pdb=" C BCT B 704 " pdb=" O2 BCT B 704 " ideal model delta sigma weight residual 1.241 1.296 -0.055 2.00e-02 2.50e+03 7.51e+00 ... (remaining 9587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 12699 3.09 - 6.18: 231 6.18 - 9.28: 19 9.28 - 12.37: 5 12.37 - 15.46: 2 Bond angle restraints: 12956 Sorted by residual: angle pdb=" C CYS A 418 " pdb=" N CYS A 419 " pdb=" CA CYS A 419 " ideal model delta sigma weight residual 121.54 133.59 -12.05 1.91e+00 2.74e-01 3.98e+01 angle pdb=" CA CYS B 633 " pdb=" CB CYS B 633 " pdb=" SG CYS B 633 " ideal model delta sigma weight residual 114.40 101.67 12.73 2.30e+00 1.89e-01 3.06e+01 angle pdb=" N ALA B 223 " pdb=" CA ALA B 223 " pdb=" C ALA B 223 " ideal model delta sigma weight residual 114.56 107.95 6.61 1.27e+00 6.20e-01 2.71e+01 angle pdb=" N MET B 27 " pdb=" CA MET B 27 " pdb=" C MET B 27 " ideal model delta sigma weight residual 114.56 108.38 6.18 1.27e+00 6.20e-01 2.37e+01 angle pdb=" N GLY B 622 " pdb=" CA GLY B 622 " pdb=" C GLY B 622 " ideal model delta sigma weight residual 113.18 123.01 -9.83 2.37e+00 1.78e-01 1.72e+01 ... (remaining 12951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5029 17.75 - 35.51: 631 35.51 - 53.26: 104 53.26 - 71.02: 16 71.02 - 88.77: 11 Dihedral angle restraints: 5791 sinusoidal: 2314 harmonic: 3477 Sorted by residual: dihedral pdb=" CA CYS B 628 " pdb=" C CYS B 628 " pdb=" N PRO B 629 " pdb=" CA PRO B 629 " ideal model delta harmonic sigma weight residual 180.00 124.60 55.40 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" CB CYS B 576 " pdb=" SG CYS B 576 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -167.15 81.15 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" CA ILE A 68 " pdb=" C ILE A 68 " pdb=" N PRO A 69 " pdb=" CA PRO A 69 " ideal model delta harmonic sigma weight residual -180.00 -138.53 -41.47 0 5.00e+00 4.00e-02 6.88e+01 ... (remaining 5788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1083 0.065 - 0.129: 274 0.129 - 0.194: 25 0.194 - 0.259: 0 0.259 - 0.323: 1 Chirality restraints: 1383 Sorted by residual: chirality pdb=" CB ILE A 672 " pdb=" CA ILE A 672 " pdb=" CG1 ILE A 672 " pdb=" CG2 ILE A 672 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CB ILE A 323 " pdb=" CA ILE A 323 " pdb=" CG1 ILE A 323 " pdb=" CG2 ILE A 323 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" CA GLN B 14 " pdb=" N GLN B 14 " pdb=" C GLN B 14 " pdb=" CB GLN B 14 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.67e-01 ... (remaining 1380 not shown) Planarity restraints: 1722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 472 " -0.052 5.00e-02 4.00e+02 7.76e-02 9.64e+00 pdb=" N PRO B 473 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 473 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 473 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 141 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO B 142 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 142 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 142 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 436 " 0.037 2.00e-02 2.50e+03 2.04e-02 8.34e+00 pdb=" CG TYR B 436 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 436 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 436 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 436 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 436 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 436 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 436 " 0.015 2.00e-02 2.50e+03 ... (remaining 1719 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 60 2.32 - 2.97: 5384 2.97 - 3.61: 13948 3.61 - 4.26: 21378 4.26 - 4.90: 35218 Nonbonded interactions: 75988 Sorted by model distance: nonbonded pdb="FE FE B 701 " pdb=" O2 BCT B 703 " model vdw 1.680 2.260 nonbonded pdb=" OH TYR B 436 " pdb="FE FE B 701 " model vdw 1.749 2.260 nonbonded pdb=" OD2 ASP B 61 " pdb=" NE2 HIS B 254 " model vdw 1.762 3.120 nonbonded pdb="FE FE B 702 " pdb=" O3 BCT B 704 " model vdw 1.862 2.260 nonbonded pdb=" OD1 ASP B 396 " pdb="FE FE B 701 " model vdw 1.878 2.260 ... (remaining 75983 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.130 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.090 Find NCS groups from input model: 0.050 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 9609 Z= 0.351 Angle : 1.045 15.460 12990 Z= 0.577 Chirality : 0.054 0.323 1383 Planarity : 0.006 0.078 1722 Dihedral : 15.397 88.771 3518 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 28.91 Ramachandran Plot: Outliers : 0.25 % Allowed : 21.44 % Favored : 78.31 % Rotamer: Outliers : 0.81 % Allowed : 9.36 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.17 % 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: -6.39 (0.16), residues: 1208 helix: -4.23 (0.19), residues: 227 sheet: -3.16 (0.29), residues: 212 loop : -4.90 (0.14), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 211 TYR 0.040 0.003 TYR B 436 PHE 0.025 0.003 PHE B 326 TRP 0.040 0.003 TRP A 183 HIS 0.014 0.002 HIS B 598 Details of bonding type rmsd covalent geometry : bond 0.00776 ( 9592) covalent geometry : angle 1.03810 (12956) SS BOND : bond 0.00997 ( 17) SS BOND : angle 2.55011 ( 34) hydrogen bonds : bond 0.15251 ( 251) hydrogen bonds : angle 8.75255 ( 672) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 117 LYS cc_start: 0.6876 (ttmt) cc_final: 0.6560 (mmtp) REVERT: B 395 LEU cc_start: 0.6276 (OUTLIER) cc_final: 0.6012 (pp) outliers start: 8 outliers final: 3 residues processed: 101 average time/residue: 0.1197 time to fit residues: 16.5192 Evaluate side-chains 70 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0170 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 30.0000 chunk 117 optimal weight: 0.8980 overall best weight: 1.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN B 45 GLN B 117 HIS B 330 GLN ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.197434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.162112 restraints weight = 16131.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.159461 restraints weight = 20137.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.161653 restraints weight = 17947.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.162462 restraints weight = 11642.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.162725 restraints weight = 10888.943| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9609 Z= 0.203 Angle : 0.850 14.143 12990 Z= 0.442 Chirality : 0.049 0.304 1383 Planarity : 0.006 0.082 1722 Dihedral : 7.993 53.507 1325 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 16.23 % Favored : 83.69 % Rotamer: Outliers : 3.05 % Allowed : 14.65 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.17 % 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: -5.43 (0.18), residues: 1208 helix: -3.47 (0.23), residues: 235 sheet: -2.53 (0.33), residues: 202 loop : -4.23 (0.17), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 211 TYR 0.026 0.002 TYR A 251 PHE 0.017 0.002 PHE B 301 TRP 0.035 0.002 TRP B 139 HIS 0.019 0.002 HIS B 598 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 9592) covalent geometry : angle 0.84291 (12956) SS BOND : bond 0.00887 ( 17) SS BOND : angle 2.36843 ( 34) hydrogen bonds : bond 0.05448 ( 251) hydrogen bonds : angle 7.26633 ( 672) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.380 Fit side-chains REVERT: A 117 LYS cc_start: 0.6477 (ttmt) cc_final: 0.6251 (mmtp) REVERT: B 27 MET cc_start: 0.7452 (tpp) cc_final: 0.7042 (mtt) REVERT: B 67 GLU cc_start: 0.5683 (OUTLIER) cc_final: 0.3828 (mp0) REVERT: B 170 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6635 (tt) REVERT: B 395 LEU cc_start: 0.6347 (OUTLIER) cc_final: 0.5833 (pp) outliers start: 30 outliers final: 17 residues processed: 124 average time/residue: 0.1090 time to fit residues: 18.7792 Evaluate side-chains 96 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 598 HIS Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 5 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 48 optimal weight: 40.0000 chunk 27 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN B 516 ASN ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.201244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.168125 restraints weight = 15510.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.166227 restraints weight = 21971.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.168157 restraints weight = 19461.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.168761 restraints weight = 13121.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.168799 restraints weight = 12107.560| |-----------------------------------------------------------------------------| r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 9609 Z= 0.185 Angle : 0.825 18.409 12990 Z= 0.428 Chirality : 0.047 0.288 1383 Planarity : 0.005 0.077 1722 Dihedral : 7.696 52.205 1325 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.65 % Favored : 85.35 % Rotamer: Outliers : 4.27 % Allowed : 18.01 % Favored : 77.72 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.77 (0.20), residues: 1208 helix: -2.92 (0.26), residues: 238 sheet: -2.27 (0.33), residues: 225 loop : -3.76 (0.19), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 534 TYR 0.015 0.002 TYR A 131 PHE 0.027 0.002 PHE B 301 TRP 0.028 0.002 TRP B 563 HIS 0.015 0.001 HIS B 598 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 9592) covalent geometry : angle 0.81909 (12956) SS BOND : bond 0.01391 ( 17) SS BOND : angle 2.15054 ( 34) hydrogen bonds : bond 0.05036 ( 251) hydrogen bonds : angle 6.99722 ( 672) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 98 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 117 LYS cc_start: 0.6495 (ttmt) cc_final: 0.6249 (mmtp) REVERT: A 205 TYR cc_start: 0.7450 (m-80) cc_final: 0.7181 (m-80) REVERT: B 27 MET cc_start: 0.7301 (tpp) cc_final: 0.6883 (mtt) REVERT: B 67 GLU cc_start: 0.5561 (OUTLIER) cc_final: 0.3734 (mp0) REVERT: B 170 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6036 (tt) REVERT: B 171 CYS cc_start: 0.3924 (OUTLIER) cc_final: 0.3528 (p) REVERT: B 395 LEU cc_start: 0.6284 (OUTLIER) cc_final: 0.5808 (pp) REVERT: B 617 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.7829 (pt0) REVERT: B 633 CYS cc_start: 0.5658 (m) cc_final: 0.5068 (p) outliers start: 42 outliers final: 19 residues processed: 132 average time/residue: 0.0858 time to fit residues: 16.6754 Evaluate side-chains 102 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain B residue 634 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 4 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 103 optimal weight: 0.4980 chunk 37 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 39 optimal weight: 30.0000 chunk 38 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.201465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.166813 restraints weight = 15797.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.165148 restraints weight = 17944.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.166986 restraints weight = 16780.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.167708 restraints weight = 10655.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.167835 restraints weight = 10073.444| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9609 Z= 0.166 Angle : 0.784 11.877 12990 Z= 0.401 Chirality : 0.046 0.279 1383 Planarity : 0.005 0.078 1722 Dihedral : 7.199 51.278 1323 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.40 % Favored : 85.51 % Rotamer: Outliers : 4.17 % Allowed : 19.84 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.43 (0.21), residues: 1208 helix: -2.60 (0.28), residues: 239 sheet: -2.37 (0.32), residues: 241 loop : -3.43 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 534 TYR 0.020 0.002 TYR A 251 PHE 0.020 0.002 PHE A 237 TRP 0.026 0.002 TRP B 563 HIS 0.010 0.001 HIS B 598 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 9592) covalent geometry : angle 0.77168 (12956) SS BOND : bond 0.00650 ( 17) SS BOND : angle 2.78288 ( 34) hydrogen bonds : bond 0.04719 ( 251) hydrogen bonds : angle 6.65892 ( 672) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 86 time to evaluate : 0.348 Fit side-chains REVERT: B 27 MET cc_start: 0.7226 (tpp) cc_final: 0.6802 (mtt) REVERT: B 37 CYS cc_start: 0.6598 (OUTLIER) cc_final: 0.6214 (m) REVERT: B 67 GLU cc_start: 0.5557 (OUTLIER) cc_final: 0.3782 (mp0) REVERT: B 170 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6682 (tt) REVERT: B 395 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.5881 (pp) REVERT: B 412 LEU cc_start: 0.5394 (OUTLIER) cc_final: 0.5150 (mm) REVERT: B 474 MET cc_start: 0.6190 (OUTLIER) cc_final: 0.5952 (mtm) REVERT: B 617 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8419 (pt0) REVERT: B 633 CYS cc_start: 0.5321 (m) cc_final: 0.4927 (p) outliers start: 41 outliers final: 25 residues processed: 119 average time/residue: 0.0887 time to fit residues: 15.4737 Evaluate side-chains 102 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 484 CYS Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 84 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 108 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 HIS ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.204051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.171279 restraints weight = 15494.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.168226 restraints weight = 20337.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.170285 restraints weight = 19935.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.170898 restraints weight = 12709.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.170967 restraints weight = 11994.874| |-----------------------------------------------------------------------------| r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9609 Z= 0.146 Angle : 0.741 12.857 12990 Z= 0.377 Chirality : 0.045 0.269 1383 Planarity : 0.005 0.078 1722 Dihedral : 6.869 50.598 1323 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.82 % Favored : 86.09 % Rotamer: Outliers : 5.09 % Allowed : 19.53 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.12 (0.22), residues: 1208 helix: -2.21 (0.29), residues: 245 sheet: -2.15 (0.33), residues: 225 loop : -3.29 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 603 TYR 0.020 0.002 TYR A 251 PHE 0.022 0.001 PHE A 237 TRP 0.028 0.002 TRP B 563 HIS 0.006 0.001 HIS B 598 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9592) covalent geometry : angle 0.73288 (12956) SS BOND : bond 0.00865 ( 17) SS BOND : angle 2.22365 ( 34) hydrogen bonds : bond 0.04268 ( 251) hydrogen bonds : angle 6.40350 ( 672) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 95 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 171 LEU cc_start: 0.8070 (tp) cc_final: 0.7868 (tp) REVERT: B 27 MET cc_start: 0.7229 (tpp) cc_final: 0.6640 (mtt) REVERT: B 67 GLU cc_start: 0.5455 (OUTLIER) cc_final: 0.3690 (mp0) REVERT: B 343 ARG cc_start: 0.7681 (mpt180) cc_final: 0.7280 (mtt90) REVERT: B 395 LEU cc_start: 0.6204 (OUTLIER) cc_final: 0.5707 (pp) REVERT: B 412 LEU cc_start: 0.5685 (OUTLIER) cc_final: 0.5420 (mm) REVERT: B 474 MET cc_start: 0.6016 (OUTLIER) cc_final: 0.5786 (mtm) REVERT: B 594 MET cc_start: 0.4191 (mpp) cc_final: 0.3838 (mpp) REVERT: B 617 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7662 (pt0) REVERT: B 633 CYS cc_start: 0.5085 (m) cc_final: 0.4839 (p) outliers start: 50 outliers final: 27 residues processed: 134 average time/residue: 0.0883 time to fit residues: 17.2682 Evaluate side-chains 111 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 484 CYS Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 7 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN B 14 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.199917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.167061 restraints weight = 15536.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.164162 restraints weight = 22690.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.166298 restraints weight = 20324.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.166821 restraints weight = 13113.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.166844 restraints weight = 12302.831| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.151 9609 Z= 0.232 Angle : 0.835 17.613 12990 Z= 0.427 Chirality : 0.048 0.272 1383 Planarity : 0.006 0.082 1722 Dihedral : 7.415 70.895 1323 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.23 % Favored : 84.69 % Rotamer: Outliers : 5.70 % Allowed : 20.35 % Favored : 73.96 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.20 (0.21), residues: 1208 helix: -2.25 (0.29), residues: 245 sheet: -2.27 (0.33), residues: 230 loop : -3.32 (0.20), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 603 TYR 0.019 0.002 TYR A 162 PHE 0.029 0.002 PHE A 237 TRP 0.018 0.002 TRP B 563 HIS 0.006 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 9592) covalent geometry : angle 0.82177 (12956) SS BOND : bond 0.01518 ( 17) SS BOND : angle 2.99310 ( 34) hydrogen bonds : bond 0.04917 ( 251) hydrogen bonds : angle 6.59795 ( 672) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 78 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 TYR cc_start: 0.7827 (p90) cc_final: 0.7606 (p90) REVERT: B 27 MET cc_start: 0.7182 (tpp) cc_final: 0.6729 (mtt) REVERT: B 67 GLU cc_start: 0.5561 (OUTLIER) cc_final: 0.3744 (mp0) REVERT: B 395 LEU cc_start: 0.6330 (OUTLIER) cc_final: 0.5973 (pp) REVERT: B 412 LEU cc_start: 0.5771 (OUTLIER) cc_final: 0.5513 (mm) outliers start: 56 outliers final: 37 residues processed: 123 average time/residue: 0.0865 time to fit residues: 15.5383 Evaluate side-chains 111 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 71 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 526 ARG Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 484 CYS Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 598 HIS Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 93 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 109 optimal weight: 0.1980 chunk 30 optimal weight: 0.0570 chunk 76 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 HIS B 624 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.203650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.170109 restraints weight = 16008.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.168723 restraints weight = 18976.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.170459 restraints weight = 16998.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.170917 restraints weight = 11171.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.170972 restraints weight = 10887.240| |-----------------------------------------------------------------------------| r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.169 9609 Z= 0.145 Angle : 0.792 18.499 12990 Z= 0.402 Chirality : 0.045 0.257 1383 Planarity : 0.005 0.077 1722 Dihedral : 6.845 50.567 1323 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.67 % Favored : 87.25 % Rotamer: Outliers : 3.87 % Allowed : 21.97 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.17 % 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: -3.84 (0.22), residues: 1208 helix: -1.85 (0.31), residues: 235 sheet: -2.17 (0.32), residues: 242 loop : -3.08 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 106 TYR 0.021 0.001 TYR B 66 PHE 0.019 0.001 PHE A 237 TRP 0.032 0.002 TRP B 563 HIS 0.007 0.001 HIS B 598 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9592) covalent geometry : angle 0.77388 (12956) SS BOND : bond 0.00848 ( 17) SS BOND : angle 3.41215 ( 34) hydrogen bonds : bond 0.04000 ( 251) hydrogen bonds : angle 6.33324 ( 672) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 MET cc_start: 0.7826 (tmm) cc_final: 0.6984 (tmm) REVERT: B 27 MET cc_start: 0.7113 (tpp) cc_final: 0.6506 (mtt) REVERT: B 67 GLU cc_start: 0.5398 (OUTLIER) cc_final: 0.3540 (mp0) REVERT: B 166 GLN cc_start: 0.6989 (OUTLIER) cc_final: 0.6745 (tp40) REVERT: B 395 LEU cc_start: 0.6032 (OUTLIER) cc_final: 0.5539 (pp) REVERT: B 412 LEU cc_start: 0.5617 (OUTLIER) cc_final: 0.5410 (mm) REVERT: B 577 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7253 (mt) REVERT: B 617 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7456 (pt0) outliers start: 38 outliers final: 26 residues processed: 125 average time/residue: 0.0918 time to fit residues: 16.4932 Evaluate side-chains 115 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 526 ARG Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 484 CYS Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 100 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 48 optimal weight: 40.0000 chunk 91 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.197447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.162704 restraints weight = 15967.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.160555 restraints weight = 23150.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.162268 restraints weight = 20384.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.163009 restraints weight = 13791.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.162914 restraints weight = 13244.582| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.141 9609 Z= 0.281 Angle : 0.884 15.628 12990 Z= 0.456 Chirality : 0.051 0.271 1383 Planarity : 0.006 0.101 1722 Dihedral : 7.452 57.518 1323 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.73 % Favored : 84.27 % Rotamer: Outliers : 4.68 % Allowed : 22.38 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 5.77 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.14 (0.22), residues: 1208 helix: -2.07 (0.30), residues: 239 sheet: -2.28 (0.32), residues: 240 loop : -3.32 (0.20), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 603 TYR 0.027 0.003 TYR A 162 PHE 0.020 0.002 PHE B 308 TRP 0.032 0.003 TRP B 470 HIS 0.008 0.002 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00662 ( 9592) covalent geometry : angle 0.86674 (12956) SS BOND : bond 0.01012 ( 17) SS BOND : angle 3.53031 ( 34) hydrogen bonds : bond 0.05273 ( 251) hydrogen bonds : angle 6.63939 ( 672) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 79 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.7229 (tpp) cc_final: 0.6846 (mtt) REVERT: B 67 GLU cc_start: 0.5549 (OUTLIER) cc_final: 0.3781 (mp0) REVERT: B 395 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.6007 (pp) REVERT: B 412 LEU cc_start: 0.5897 (OUTLIER) cc_final: 0.5626 (mm) REVERT: B 634 LEU cc_start: 0.5861 (OUTLIER) cc_final: 0.5092 (pp) outliers start: 46 outliers final: 36 residues processed: 117 average time/residue: 0.0974 time to fit residues: 16.1163 Evaluate side-chains 113 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 73 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 526 ARG Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 484 CYS Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.207327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.174832 restraints weight = 15937.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.172343 restraints weight = 22093.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.174335 restraints weight = 18849.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.175102 restraints weight = 13949.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.175150 restraints weight = 12940.307| |-----------------------------------------------------------------------------| r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 9609 Z= 0.161 Angle : 0.793 15.570 12990 Z= 0.403 Chirality : 0.046 0.253 1383 Planarity : 0.005 0.085 1722 Dihedral : 7.011 57.260 1323 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.08 % Favored : 86.92 % Rotamer: Outliers : 4.07 % Allowed : 23.30 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.17 % 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: -3.83 (0.22), residues: 1208 helix: -1.77 (0.32), residues: 233 sheet: -2.18 (0.32), residues: 240 loop : -3.09 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 52 TYR 0.013 0.002 TYR A 251 PHE 0.015 0.001 PHE A 60 TRP 0.027 0.002 TRP B 563 HIS 0.007 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 9592) covalent geometry : angle 0.77849 (12956) SS BOND : bond 0.00875 ( 17) SS BOND : angle 3.02705 ( 34) hydrogen bonds : bond 0.04269 ( 251) hydrogen bonds : angle 6.38131 ( 672) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 85 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 TYR cc_start: 0.7346 (m-80) cc_final: 0.7009 (m-80) REVERT: B 27 MET cc_start: 0.6981 (tpp) cc_final: 0.6547 (mtt) REVERT: B 67 GLU cc_start: 0.5526 (OUTLIER) cc_final: 0.3886 (mp0) REVERT: B 395 LEU cc_start: 0.6259 (OUTLIER) cc_final: 0.5805 (pp) REVERT: B 412 LEU cc_start: 0.5532 (OUTLIER) cc_final: 0.5332 (mm) REVERT: B 563 TRP cc_start: 0.6863 (p-90) cc_final: 0.6468 (p-90) REVERT: B 634 LEU cc_start: 0.5566 (OUTLIER) cc_final: 0.5015 (pp) outliers start: 40 outliers final: 32 residues processed: 119 average time/residue: 0.0884 time to fit residues: 15.4821 Evaluate side-chains 117 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 81 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 526 ARG Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 484 CYS Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 6 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 77 optimal weight: 0.0870 chunk 76 optimal weight: 2.9990 chunk 25 optimal weight: 0.0470 chunk 60 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN B 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.209921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.177472 restraints weight = 16078.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.174312 restraints weight = 21556.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.176516 restraints weight = 18031.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.177384 restraints weight = 12836.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.177488 restraints weight = 11595.056| |-----------------------------------------------------------------------------| r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 9609 Z= 0.143 Angle : 0.770 15.021 12990 Z= 0.391 Chirality : 0.045 0.253 1383 Planarity : 0.005 0.083 1722 Dihedral : 6.705 56.091 1323 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.00 % Favored : 87.00 % Rotamer: Outliers : 3.76 % Allowed : 23.40 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.17 % 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: -3.61 (0.22), residues: 1208 helix: -1.60 (0.32), residues: 235 sheet: -1.99 (0.33), residues: 240 loop : -2.96 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 333 TYR 0.013 0.001 TYR B 94 PHE 0.023 0.001 PHE B 301 TRP 0.029 0.002 TRP B 563 HIS 0.007 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9592) covalent geometry : angle 0.75720 (12956) SS BOND : bond 0.00868 ( 17) SS BOND : angle 2.83252 ( 34) hydrogen bonds : bond 0.03945 ( 251) hydrogen bonds : angle 6.28468 ( 672) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 87 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 TYR cc_start: 0.7263 (m-80) cc_final: 0.6973 (m-80) REVERT: A 413 MET cc_start: 0.7388 (tmm) cc_final: 0.6628 (tmm) REVERT: B 27 MET cc_start: 0.7215 (tpp) cc_final: 0.6560 (mtt) REVERT: B 67 GLU cc_start: 0.5384 (OUTLIER) cc_final: 0.3796 (mp0) REVERT: B 395 LEU cc_start: 0.6183 (OUTLIER) cc_final: 0.5670 (pp) REVERT: B 563 TRP cc_start: 0.6703 (p-90) cc_final: 0.6393 (p-90) REVERT: B 617 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7295 (pt0) REVERT: B 634 LEU cc_start: 0.5412 (OUTLIER) cc_final: 0.4857 (pp) outliers start: 37 outliers final: 29 residues processed: 119 average time/residue: 0.0911 time to fit residues: 15.7943 Evaluate side-chains 115 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 82 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 526 ARG Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 484 CYS Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 114 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 6 optimal weight: 0.0870 chunk 104 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 89 optimal weight: 0.3980 chunk 65 optimal weight: 0.0970 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.206583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.173100 restraints weight = 15760.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.170253 restraints weight = 20296.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.171798 restraints weight = 17026.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.172650 restraints weight = 13213.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.173489 restraints weight = 12910.131| |-----------------------------------------------------------------------------| r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.123 9609 Z= 0.141 Angle : 0.777 15.645 12990 Z= 0.390 Chirality : 0.045 0.249 1383 Planarity : 0.005 0.079 1722 Dihedral : 6.560 55.065 1323 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.42 % Favored : 87.58 % Rotamer: Outliers : 3.66 % Allowed : 24.31 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.17 % 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: -3.48 (0.23), residues: 1208 helix: -1.46 (0.32), residues: 235 sheet: -1.92 (0.33), residues: 240 loop : -2.87 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 333 TYR 0.012 0.001 TYR B 83 PHE 0.028 0.001 PHE B 644 TRP 0.027 0.002 TRP B 563 HIS 0.007 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9592) covalent geometry : angle 0.76472 (12956) SS BOND : bond 0.00859 ( 17) SS BOND : angle 2.80898 ( 34) hydrogen bonds : bond 0.03862 ( 251) hydrogen bonds : angle 6.19835 ( 672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1497.99 seconds wall clock time: 26 minutes 47.88 seconds (1607.88 seconds total)