Starting phenix.real_space_refine on Fri Mar 14 01:50:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n88_24233/03_2025/7n88_24233.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n88_24233/03_2025/7n88_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_2025/7n88_24233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n88_24233/03_2025/7n88_24233.map" model { file = "/net/cci-nas-00/data/ceres_data/7n88_24233/03_2025/7n88_24233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n88_24233/03_2025/7n88_24233.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 5, 'ASP:plan': 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: 5.85, per 1000 atoms: 0.62 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: 2.61 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.10 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: 2.88 Time building geometry restraints manager: 3.04 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: 1.000 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: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.940 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.580 ------------------------------------------------------------------------------- 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 9592 Z= 0.502 Angle : 1.038 15.460 12956 Z= 0.574 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.040 0.003 TRP A 183 HIS 0.014 0.002 HIS B 598 PHE 0.025 0.003 PHE B 326 TYR 0.040 0.003 TYR B 436 ARG 0.012 0.001 ARG B 211 *********************** 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 : 1.086 Fit side-chains revert: symmetry clash REVERT: A 117 LYS cc_start: 0.6876 (ttmt) cc_final: 0.6559 (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: 0.2674 time to fit residues: 36.9679 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 : 0.937 ------------------------------------------------------------------------------- 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 102 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 0.0050 chunk 48 optimal weight: 20.0000 chunk 94 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 136 ASN B 45 GLN B 117 HIS ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.200509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.165431 restraints weight = 15912.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.163962 restraints weight = 20143.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.165963 restraints weight = 16834.377| |-----------------------------------------------------------------------------| r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9592 Z= 0.239 Angle : 0.810 13.540 12956 Z= 0.421 Chirality : 0.047 0.300 1383 Planarity : 0.006 0.080 1722 Dihedral : 7.704 52.662 1325 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.49 % Favored : 85.43 % Rotamer: Outliers : 2.64 % Allowed : 14.14 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.36 (0.18), residues: 1208 helix: -3.37 (0.23), residues: 235 sheet: -2.61 (0.31), residues: 218 loop : -4.17 (0.17), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 139 HIS 0.018 0.001 HIS B 598 PHE 0.016 0.002 PHE B 287 TYR 0.022 0.002 TYR A 251 ARG 0.008 0.001 ARG B 211 *********************** 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 136 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 1.477 Fit side-chains REVERT: B 27 MET cc_start: 0.7460 (tpp) cc_final: 0.6966 (mtt) REVERT: B 67 GLU cc_start: 0.5618 (OUTLIER) cc_final: 0.3759 (mp0) REVERT: B 170 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6704 (tt) REVERT: B 395 LEU cc_start: 0.5883 (OUTLIER) cc_final: 0.5415 (pp) outliers start: 26 outliers final: 12 residues processed: 133 average time/residue: 0.2578 time to fit residues: 47.6587 Evaluate side-chains 90 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 405 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 170 LEU 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 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 1 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 73 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 385 HIS B 330 GLN ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.201739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.167959 restraints weight = 15873.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.164776 restraints weight = 22647.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.166951 restraints weight = 19413.527| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 9592 Z= 0.282 Angle : 0.821 18.603 12956 Z= 0.425 Chirality : 0.048 0.288 1383 Planarity : 0.005 0.076 1722 Dihedral : 7.615 51.753 1325 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.98 % Favored : 85.02 % Rotamer: Outliers : 4.17 % Allowed : 17.60 % Favored : 78.23 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.75 (0.20), residues: 1208 helix: -2.83 (0.26), residues: 238 sheet: -2.26 (0.33), residues: 216 loop : -3.77 (0.19), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 563 HIS 0.015 0.001 HIS B 598 PHE 0.014 0.002 PHE B 308 TYR 0.020 0.002 TYR B 66 ARG 0.003 0.000 ARG B 603 *********************** 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 138 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 97 time to evaluate : 1.377 Fit side-chains revert: symmetry clash REVERT: A 205 TYR cc_start: 0.7378 (m-80) cc_final: 0.7144 (m-80) REVERT: B 27 MET cc_start: 0.7466 (tpp) cc_final: 0.7052 (mtt) REVERT: B 67 GLU cc_start: 0.5571 (OUTLIER) cc_final: 0.3664 (mp0) REVERT: B 170 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6054 (tt) REVERT: B 395 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.5876 (pp) outliers start: 41 outliers final: 25 residues processed: 130 average time/residue: 0.2116 time to fit residues: 40.3264 Evaluate side-chains 107 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 323 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR 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 37 CYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 82 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 210 ILE 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 107 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 40.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 516 ASN ** B 598 HIS ** 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 = 0.4605 r_free = 0.4605 target = 0.200633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.168263 restraints weight = 15496.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.165568 restraints weight = 21889.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.167566 restraints weight = 20498.880| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9592 Z= 0.290 Angle : 0.793 13.524 12956 Z= 0.408 Chirality : 0.047 0.281 1383 Planarity : 0.005 0.079 1722 Dihedral : 7.452 51.088 1325 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.15 % Favored : 84.77 % Rotamer: Outliers : 4.78 % Allowed : 19.33 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.21), residues: 1208 helix: -2.57 (0.28), residues: 238 sheet: -2.41 (0.32), residues: 228 loop : -3.45 (0.20), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 563 HIS 0.013 0.001 HIS B 598 PHE 0.030 0.002 PHE B 644 TYR 0.022 0.002 TYR A 251 ARG 0.003 0.000 ARG B 211 *********************** 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 133 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 86 time to evaluate : 0.947 Fit side-chains REVERT: A 205 TYR cc_start: 0.7324 (m-80) cc_final: 0.7084 (m-80) REVERT: B 27 MET cc_start: 0.7256 (tpp) cc_final: 0.6882 (mtt) REVERT: B 37 CYS cc_start: 0.6589 (OUTLIER) cc_final: 0.6177 (m) REVERT: B 67 GLU cc_start: 0.5550 (OUTLIER) cc_final: 0.3661 (mp0) REVERT: B 395 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.6131 (pp) REVERT: B 412 LEU cc_start: 0.5829 (OUTLIER) cc_final: 0.5565 (mm) REVERT: B 547 LYS cc_start: 0.8259 (ttpp) cc_final: 0.8026 (ttmt) REVERT: B 633 CYS cc_start: 0.5784 (m) cc_final: 0.5329 (p) outliers start: 47 outliers final: 28 residues processed: 127 average time/residue: 0.1990 time to fit residues: 36.6816 Evaluate side-chains 107 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 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 418 CYS 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 118 THR Chi-restraints excluded: chain B residue 140 THR 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 19 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN B 331 ASN B 598 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.201287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.166182 restraints weight = 15967.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.164536 restraints weight = 19191.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.166506 restraints weight = 17947.018| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.155 9592 Z= 0.246 Angle : 0.779 17.517 12956 Z= 0.398 Chirality : 0.046 0.271 1383 Planarity : 0.005 0.078 1722 Dihedral : 7.262 52.043 1325 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.07 % Favored : 85.93 % Rotamer: Outliers : 4.98 % Allowed : 20.24 % Favored : 74.77 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.21), residues: 1208 helix: -2.29 (0.29), residues: 245 sheet: -2.33 (0.32), residues: 228 loop : -3.27 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 563 HIS 0.012 0.001 HIS B 598 PHE 0.021 0.002 PHE B 644 TYR 0.019 0.002 TYR B 66 ARG 0.004 0.000 ARG B 172 *********************** 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: 49 poor density : 96 time to evaluate : 1.098 Fit side-chains REVERT: B 27 MET cc_start: 0.7139 (tpp) cc_final: 0.6703 (mtt) REVERT: B 37 CYS cc_start: 0.6658 (OUTLIER) cc_final: 0.6246 (m) REVERT: B 67 GLU cc_start: 0.5492 (OUTLIER) cc_final: 0.3542 (mp0) REVERT: B 395 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.5933 (pp) REVERT: B 412 LEU cc_start: 0.5608 (OUTLIER) cc_final: 0.5335 (mm) REVERT: B 617 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8310 (pt0) REVERT: B 633 CYS cc_start: 0.5420 (m) cc_final: 0.5072 (p) outliers start: 49 outliers final: 27 residues processed: 136 average time/residue: 0.1991 time to fit residues: 39.5322 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 : 1.086 ------------------------------------------------------------------------------- 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 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 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 461 HIS 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 32 optimal weight: 4.9990 chunk 94 optimal weight: 0.0470 chunk 49 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 40 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.203516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.171168 restraints weight = 15414.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.169755 restraints weight = 20107.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.171209 restraints weight = 18841.749| |-----------------------------------------------------------------------------| r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 9592 Z= 0.235 Angle : 0.736 11.743 12956 Z= 0.378 Chirality : 0.046 0.268 1383 Planarity : 0.005 0.079 1722 Dihedral : 6.998 50.328 1323 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.40 % Favored : 85.51 % Rotamer: Outliers : 4.98 % Allowed : 20.24 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.22), residues: 1208 helix: -2.22 (0.29), residues: 245 sheet: -2.20 (0.32), residues: 239 loop : -3.20 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 563 HIS 0.006 0.001 HIS B 598 PHE 0.025 0.002 PHE A 237 TYR 0.020 0.002 TYR A 131 ARG 0.002 0.000 ARG B 603 *********************** 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 138 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 89 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.6962 (tpp) cc_final: 0.6518 (mtt) REVERT: B 67 GLU cc_start: 0.5509 (OUTLIER) cc_final: 0.3678 (mp0) REVERT: B 343 ARG cc_start: 0.7516 (mpt180) cc_final: 0.7099 (mtt90) REVERT: B 395 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.6008 (pp) REVERT: B 412 LEU cc_start: 0.5609 (OUTLIER) cc_final: 0.5351 (mm) REVERT: B 594 MET cc_start: 0.4188 (mpp) cc_final: 0.3857 (mpp) REVERT: B 633 CYS cc_start: 0.5152 (m) cc_final: 0.4928 (p) outliers start: 49 outliers final: 36 residues processed: 128 average time/residue: 0.1912 time to fit residues: 35.7125 Evaluate side-chains 119 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 80 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 203 LEU 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 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 120 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 253 SER 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 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 6 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 39 optimal weight: 30.0000 chunk 40 optimal weight: 9.9990 chunk 37 optimal weight: 30.0000 chunk 93 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.200848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.168453 restraints weight = 15857.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.165894 restraints weight = 20550.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.167663 restraints weight = 19608.177| |-----------------------------------------------------------------------------| r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9592 Z= 0.313 Angle : 0.776 11.851 12956 Z= 0.399 Chirality : 0.047 0.266 1383 Planarity : 0.005 0.081 1722 Dihedral : 7.220 51.035 1323 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.07 % Favored : 84.93 % Rotamer: Outliers : 5.09 % Allowed : 20.96 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.22), residues: 1208 helix: -2.26 (0.29), residues: 245 sheet: -2.19 (0.32), residues: 239 loop : -3.24 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 563 HIS 0.006 0.001 HIS A 299 PHE 0.020 0.002 PHE A 237 TYR 0.031 0.002 TYR B 527 ARG 0.004 0.000 ARG B 603 *********************** 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 134 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 84 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.7103 (tpp) cc_final: 0.6689 (mtt) REVERT: B 67 GLU cc_start: 0.5437 (OUTLIER) cc_final: 0.3649 (mp0) REVERT: B 343 ARG cc_start: 0.7568 (mpt180) cc_final: 0.7151 (mtt90) REVERT: B 395 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.6044 (pp) REVERT: B 412 LEU cc_start: 0.5713 (OUTLIER) cc_final: 0.5443 (mm) REVERT: B 594 MET cc_start: 0.4220 (mpp) cc_final: 0.3923 (mpp) outliers start: 50 outliers final: 38 residues processed: 125 average time/residue: 0.1977 time to fit residues: 35.6953 Evaluate side-chains 113 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 72 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 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 271 LEU 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 120 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 210 ILE 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 58 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 119 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 39 optimal weight: 20.0000 chunk 41 optimal weight: 0.4980 chunk 100 optimal weight: 2.9990 chunk 51 optimal weight: 0.0870 chunk 20 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN B 616 HIS B 624 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.203241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.168710 restraints weight = 16131.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.167551 restraints weight = 19185.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.169230 restraints weight = 16755.960| |-----------------------------------------------------------------------------| r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 9592 Z= 0.204 Angle : 0.757 18.311 12956 Z= 0.383 Chirality : 0.045 0.255 1383 Planarity : 0.005 0.078 1722 Dihedral : 6.801 50.721 1323 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % Rotamer: Outliers : 3.15 % Allowed : 23.80 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.22), residues: 1208 helix: -1.86 (0.31), residues: 233 sheet: -2.07 (0.33), residues: 240 loop : -3.04 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 563 HIS 0.005 0.001 HIS B 598 PHE 0.030 0.001 PHE A 237 TYR 0.028 0.002 TYR B 527 ARG 0.002 0.000 ARG A 56 *********************** 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 133 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 TYR cc_start: 0.7242 (m-80) cc_final: 0.7009 (m-80) REVERT: A 413 MET cc_start: 0.7748 (tmm) cc_final: 0.6678 (tmm) REVERT: B 27 MET cc_start: 0.7158 (tpp) cc_final: 0.6578 (mtt) REVERT: B 67 GLU cc_start: 0.5303 (OUTLIER) cc_final: 0.3577 (mp0) REVERT: B 343 ARG cc_start: 0.7570 (mpt180) cc_final: 0.7157 (mtt90) REVERT: B 395 LEU cc_start: 0.6303 (OUTLIER) cc_final: 0.5835 (pp) REVERT: B 412 LEU cc_start: 0.5528 (OUTLIER) cc_final: 0.5317 (mm) outliers start: 31 outliers final: 23 residues processed: 128 average time/residue: 0.2108 time to fit residues: 39.1195 Evaluate side-chains 109 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 203 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 PHE 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 120 LEU Chi-restraints excluded: chain B residue 140 THR 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 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 63 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.200710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.165837 restraints weight = 16022.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.162634 restraints weight = 22008.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.164420 restraints weight = 18105.300| |-----------------------------------------------------------------------------| r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9592 Z= 0.275 Angle : 0.779 15.683 12956 Z= 0.399 Chirality : 0.047 0.278 1383 Planarity : 0.005 0.093 1722 Dihedral : 6.943 56.058 1323 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.82 % Favored : 86.18 % Rotamer: Outliers : 3.87 % Allowed : 23.80 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.22), residues: 1208 helix: -1.89 (0.31), residues: 240 sheet: -2.05 (0.33), residues: 240 loop : -3.03 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 470 HIS 0.007 0.001 HIS B 616 PHE 0.032 0.002 PHE A 237 TYR 0.025 0.002 TYR B 527 ARG 0.003 0.000 ARG B 603 *********************** 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 126 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 88 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 TYR cc_start: 0.7311 (m-80) cc_final: 0.7055 (m-80) REVERT: B 27 MET cc_start: 0.7324 (tpp) cc_final: 0.6772 (mtt) REVERT: B 67 GLU cc_start: 0.5470 (OUTLIER) cc_final: 0.3711 (mp0) REVERT: B 343 ARG cc_start: 0.7593 (mpt180) cc_final: 0.7194 (mtt90) REVERT: B 395 LEU cc_start: 0.6224 (OUTLIER) cc_final: 0.5894 (pp) REVERT: B 634 LEU cc_start: 0.5550 (OUTLIER) cc_final: 0.5022 (pp) outliers start: 38 outliers final: 29 residues processed: 119 average time/residue: 0.2790 time to fit residues: 46.8137 Evaluate side-chains 113 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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 203 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 271 LEU 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 120 LEU Chi-restraints excluded: chain B residue 140 THR 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 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 31 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 116 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.201523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.168071 restraints weight = 15894.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.165143 restraints weight = 23502.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.167147 restraints weight = 20096.144| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9592 Z= 0.287 Angle : 0.782 15.150 12956 Z= 0.399 Chirality : 0.048 0.255 1383 Planarity : 0.005 0.091 1722 Dihedral : 6.929 56.725 1323 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.65 % Favored : 85.35 % Rotamer: Outliers : 3.66 % Allowed : 24.21 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.22), residues: 1208 helix: -1.84 (0.31), residues: 238 sheet: -2.08 (0.32), residues: 240 loop : -3.00 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 470 HIS 0.007 0.001 HIS B 616 PHE 0.029 0.002 PHE A 237 TYR 0.024 0.002 TYR B 527 ARG 0.002 0.000 ARG B 603 ********************** 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 121 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 85 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 TYR cc_start: 0.7373 (m-80) cc_final: 0.7052 (m-80) REVERT: A 413 MET cc_start: 0.7774 (tmm) cc_final: 0.6513 (tmm) REVERT: B 27 MET cc_start: 0.7284 (tpp) cc_final: 0.6748 (mtt) REVERT: B 67 GLU cc_start: 0.5424 (OUTLIER) cc_final: 0.3573 (mp0) REVERT: B 343 ARG cc_start: 0.7582 (mpt180) cc_final: 0.7174 (mtt90) REVERT: B 395 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6465 (pp) REVERT: B 634 LEU cc_start: 0.5584 (OUTLIER) cc_final: 0.5022 (pp) outliers start: 36 outliers final: 30 residues processed: 114 average time/residue: 0.2752 time to fit residues: 45.9245 Evaluate side-chains 113 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 203 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 271 LEU 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 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 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 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 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 80 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 108 optimal weight: 0.0870 chunk 6 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 50 optimal weight: 9.9990 chunk 48 optimal weight: 40.0000 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.204476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.168405 restraints weight = 15877.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.167437 restraints weight = 16553.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.169808 restraints weight = 14518.941| |-----------------------------------------------------------------------------| r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9592 Z= 0.217 Angle : 0.749 14.159 12956 Z= 0.381 Chirality : 0.046 0.248 1383 Planarity : 0.005 0.083 1722 Dihedral : 6.705 54.439 1323 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 3.26 % Allowed : 24.31 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.23), residues: 1208 helix: -1.58 (0.32), residues: 236 sheet: -1.83 (0.34), residues: 229 loop : -2.93 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 563 HIS 0.007 0.001 HIS B 616 PHE 0.022 0.001 PHE B 301 TYR 0.024 0.002 TYR B 527 ARG 0.002 0.000 ARG A 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2938.63 seconds wall clock time: 53 minutes 13.50 seconds (3193.50 seconds total)