Starting phenix.real_space_refine on Thu Feb 13 22:08:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n88_24233/02_2025/7n88_24233.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n88_24233/02_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_24233/02_2025/7n88_24233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n88_24233/02_2025/7n88_24233.map" model { file = "/net/cci-nas-00/data/ceres_data/7n88_24233/02_2025/7n88_24233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n88_24233/02_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-5592/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: 5.34, per 1000 atoms: 0.57 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: 2.48 Conformation dependent library (CDL) restraints added in 1.1 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: 1.11 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: 2.85 Time building geometry restraints manager: 2.90 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: 0.870 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: 0.250 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.860 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.740 ------------------------------------------------------------------------------- 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 : 1.118 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: 0.2621 time to fit residues: 36.5523 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 : 1.234 ------------------------------------------------------------------------------- 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 = 15912.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.163963 restraints weight = 20145.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.165959 restraints weight = 16835.958| |-----------------------------------------------------------------------------| 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 : 0.993 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: 0.2439 time to fit residues: 44.2925 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 : 1.114 ------------------------------------------------------------------------------- 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: 0.0970 chunk 73 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 48 optimal weight: 40.0000 chunk 36 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN B 598 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.201906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.168128 restraints weight = 15866.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.164930 restraints weight = 22769.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.167137 restraints weight = 19398.411| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 9592 Z= 0.272 Angle : 0.821 19.179 12956 Z= 0.425 Chirality : 0.048 0.289 1383 Planarity : 0.005 0.076 1722 Dihedral : 7.605 51.770 1325 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.82 % Favored : 85.18 % Rotamer: Outliers : 4.27 % Allowed : 17.60 % Favored : 78.13 % 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: -4.74 (0.20), residues: 1208 helix: -2.83 (0.26), residues: 238 sheet: -2.25 (0.33), residues: 216 loop : -3.76 (0.19), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 563 HIS 0.014 0.001 HIS B 598 PHE 0.014 0.002 PHE B 308 TYR 0.021 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 142 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 100 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 TYR cc_start: 0.7364 (m-80) cc_final: 0.7144 (m-80) REVERT: B 27 MET cc_start: 0.7458 (tpp) cc_final: 0.7039 (mtt) REVERT: B 67 GLU cc_start: 0.5549 (OUTLIER) cc_final: 0.3638 (mp0) REVERT: B 170 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6107 (tt) REVERT: B 395 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.5867 (pp) REVERT: B 633 CYS cc_start: 0.5732 (m) cc_final: 0.5202 (p) outliers start: 42 outliers final: 25 residues processed: 134 average time/residue: 0.2166 time to fit residues: 42.0475 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 : 1.075 ------------------------------------------------------------------------------- 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 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 598 HIS 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: 2.9990 chunk 88 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 82 optimal weight: 0.3980 chunk 108 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 HIS B 516 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 = 0.4589 r_free = 0.4589 target = 0.199142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.166455 restraints weight = 15533.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.163367 restraints weight = 23340.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.165533 restraints weight = 20822.074| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 9592 Z= 0.358 Angle : 0.829 12.765 12956 Z= 0.428 Chirality : 0.049 0.285 1383 Planarity : 0.006 0.083 1722 Dihedral : 7.662 51.525 1325 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.56 % Favored : 84.35 % Rotamer: Outliers : 4.88 % Allowed : 18.92 % Favored : 76.20 % 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: -4.55 (0.21), residues: 1208 helix: -2.67 (0.27), residues: 238 sheet: -2.38 (0.33), residues: 225 loop : -3.55 (0.19), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 563 HIS 0.009 0.001 HIS B 598 PHE 0.028 0.002 PHE B 644 TYR 0.023 0.003 TYR A 251 ARG 0.004 0.000 ARG B 534 *********************** 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 128 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 80 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 205 TYR cc_start: 0.7364 (m-80) cc_final: 0.7027 (m-80) REVERT: B 27 MET cc_start: 0.7332 (tpp) cc_final: 0.6959 (mtt) REVERT: B 37 CYS cc_start: 0.6593 (OUTLIER) cc_final: 0.6188 (m) REVERT: B 67 GLU cc_start: 0.5577 (OUTLIER) cc_final: 0.3728 (mp0) REVERT: B 170 LEU cc_start: 0.6114 (OUTLIER) cc_final: 0.5911 (tt) REVERT: B 395 LEU cc_start: 0.6195 (OUTLIER) cc_final: 0.5871 (pp) REVERT: B 617 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8170 (pt0) REVERT: B 633 CYS cc_start: 0.5668 (m) cc_final: 0.5173 (p) outliers start: 48 outliers final: 29 residues processed: 121 average time/residue: 0.1960 time to fit residues: 34.5912 Evaluate side-chains 103 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 69 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 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 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 210 ILE 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 437 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: 0.6980 chunk 79 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 71 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 61 optimal weight: 0.0370 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.202298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.167574 restraints weight = 15966.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.166771 restraints weight = 18625.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.168542 restraints weight = 15891.590| |-----------------------------------------------------------------------------| r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 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 0.156 9592 Z= 0.226 Angle : 0.776 17.557 12956 Z= 0.395 Chirality : 0.045 0.271 1383 Planarity : 0.005 0.077 1722 Dihedral : 7.227 51.292 1325 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer: Outliers : 4.48 % Allowed : 20.35 % Favored : 75.18 % 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: -4.22 (0.21), residues: 1208 helix: -2.36 (0.29), residues: 239 sheet: -2.25 (0.33), residues: 219 loop : -3.31 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 563 HIS 0.004 0.001 HIS B 598 PHE 0.021 0.001 PHE B 644 TYR 0.020 0.002 TYR A 251 ARG 0.003 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 137 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 93 time to evaluate : 1.007 Fit side-chains REVERT: B 27 MET cc_start: 0.7208 (tpp) cc_final: 0.6672 (mtt) REVERT: B 37 CYS cc_start: 0.6658 (OUTLIER) cc_final: 0.6253 (m) REVERT: B 67 GLU cc_start: 0.5490 (OUTLIER) cc_final: 0.3645 (mp0) REVERT: B 395 LEU cc_start: 0.6189 (OUTLIER) cc_final: 0.5701 (pp) REVERT: B 474 MET cc_start: 0.6004 (OUTLIER) cc_final: 0.5730 (mtm) REVERT: B 633 CYS cc_start: 0.5418 (m) cc_final: 0.5079 (p) outliers start: 44 outliers final: 26 residues processed: 131 average time/residue: 0.2043 time to fit residues: 38.8486 Evaluate side-chains 106 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 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 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 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 474 MET Chi-restraints excluded: chain B residue 484 CYS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 690 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 32 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 33 optimal weight: 0.0000 chunk 97 optimal weight: 0.0170 chunk 54 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 112 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 overall best weight: 0.5226 ------------------------------------------------------------------------------- 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 = 0.4658 r_free = 0.4658 target = 0.205711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.172376 restraints weight = 15441.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.169983 restraints weight = 17978.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.172191 restraints weight = 16365.490| |-----------------------------------------------------------------------------| r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9592 Z= 0.198 Angle : 0.722 11.355 12956 Z= 0.368 Chirality : 0.046 0.267 1383 Planarity : 0.005 0.078 1722 Dihedral : 6.829 49.915 1323 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.00 % Favored : 86.92 % Rotamer: Outliers : 4.37 % Allowed : 20.65 % Favored : 74.97 % 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: -3.97 (0.22), residues: 1208 helix: -2.12 (0.29), residues: 247 sheet: -2.06 (0.34), residues: 226 loop : -3.17 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 563 HIS 0.004 0.001 HIS B 598 PHE 0.025 0.001 PHE A 237 TYR 0.020 0.002 TYR A 131 ARG 0.005 0.000 ARG B 172 *********************** 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 137 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 94 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.7269 (tpp) cc_final: 0.6682 (mtt) REVERT: B 67 GLU cc_start: 0.5406 (OUTLIER) cc_final: 0.3409 (mp0) REVERT: B 395 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5708 (pp) REVERT: B 474 MET cc_start: 0.5980 (OUTLIER) cc_final: 0.5734 (mtm) outliers start: 43 outliers final: 28 residues processed: 127 average time/residue: 0.2048 time to fit residues: 37.8201 Evaluate side-chains 113 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 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 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 140 THR Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 266 ASP 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 474 MET Chi-restraints excluded: chain B residue 484 CYS Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 646 ASP Chi-restraints excluded: chain B residue 690 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 6 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 30.0000 chunk 40 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 314 ASN B 331 ASN ** B 624 ASN ** 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 = 0.4622 r_free = 0.4622 target = 0.202125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.167428 restraints weight = 15905.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.164217 restraints weight = 20796.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.166057 restraints weight = 17352.889| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9592 Z= 0.292 Angle : 0.788 17.065 12956 Z= 0.402 Chirality : 0.047 0.267 1383 Planarity : 0.005 0.090 1722 Dihedral : 7.055 49.568 1323 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.24 % Favored : 85.76 % Rotamer: Outliers : 5.09 % Allowed : 21.46 % Favored : 73.45 % 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: -3.99 (0.22), residues: 1208 helix: -2.07 (0.30), residues: 246 sheet: -2.18 (0.32), residues: 240 loop : -3.18 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 563 HIS 0.005 0.001 HIS A 299 PHE 0.017 0.002 PHE A 237 TYR 0.016 0.002 TYR A 162 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 141 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 91 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.7315 (tpp) cc_final: 0.6741 (mtt) REVERT: B 67 GLU cc_start: 0.5494 (OUTLIER) cc_final: 0.3601 (mp0) REVERT: B 395 LEU cc_start: 0.6231 (OUTLIER) cc_final: 0.5899 (pp) outliers start: 50 outliers final: 37 residues processed: 129 average time/residue: 0.2107 time to fit residues: 38.8834 Evaluate side-chains 118 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 79 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 12 VAL Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 67 GLU 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 331 ASN 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 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 589 SER Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 613 VAL 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: 4.9990 chunk 115 optimal weight: 0.0000 chunk 84 optimal weight: 0.0570 chunk 37 optimal weight: 0.4980 chunk 119 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 39 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 51 optimal weight: 40.0000 chunk 20 optimal weight: 5.9990 overall best weight: 0.4302 ------------------------------------------------------------------------------- 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 B 616 HIS B 624 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.204636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.171791 restraints weight = 16160.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.171229 restraints weight = 19917.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.173163 restraints weight = 17213.956| |-----------------------------------------------------------------------------| r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9592 Z= 0.199 Angle : 0.745 16.980 12956 Z= 0.377 Chirality : 0.045 0.255 1383 Planarity : 0.005 0.077 1722 Dihedral : 6.720 55.487 1323 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % Rotamer: Outliers : 3.66 % Allowed : 23.19 % Favored : 73.14 % 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: -3.66 (0.22), residues: 1208 helix: -1.64 (0.32), residues: 233 sheet: -2.04 (0.33), residues: 240 loop : -2.97 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 563 HIS 0.005 0.001 HIS B 598 PHE 0.031 0.001 PHE A 237 TYR 0.014 0.001 TYR B 94 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 137 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 MET cc_start: 0.7552 (tmm) cc_final: 0.6753 (tmm) REVERT: B 67 GLU cc_start: 0.5348 (OUTLIER) cc_final: 0.3641 (mp0) REVERT: B 395 LEU cc_start: 0.6020 (OUTLIER) cc_final: 0.5518 (pp) REVERT: B 563 TRP cc_start: 0.6760 (p-90) cc_final: 0.6554 (p-90) REVERT: B 634 LEU cc_start: 0.5634 (OUTLIER) cc_final: 0.5073 (pp) outliers start: 36 outliers final: 25 residues processed: 131 average time/residue: 0.2225 time to fit residues: 42.4117 Evaluate side-chains 114 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 63 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 81 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 ** 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 = 0.4723 r_free = 0.4723 target = 0.211724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.180843 restraints weight = 16155.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.178141 restraints weight = 18606.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.179969 restraints weight = 18191.698| |-----------------------------------------------------------------------------| r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9592 Z= 0.198 Angle : 0.751 14.923 12956 Z= 0.381 Chirality : 0.046 0.262 1383 Planarity : 0.005 0.078 1722 Dihedral : 6.602 55.900 1323 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 3.05 % Allowed : 23.80 % Favored : 73.14 % 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: -3.52 (0.22), residues: 1208 helix: -1.48 (0.33), residues: 233 sheet: -1.97 (0.33), residues: 240 loop : -2.90 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 563 HIS 0.007 0.001 HIS B 616 PHE 0.040 0.001 PHE A 237 TYR 0.013 0.001 TYR A 251 ARG 0.004 0.000 ARG B 172 *********************** 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: 30 poor density : 96 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: A 526 ARG cc_start: 0.2790 (OUTLIER) cc_final: 0.0274 (mmt90) REVERT: B 67 GLU cc_start: 0.5433 (OUTLIER) cc_final: 0.3615 (mp0) REVERT: B 170 LEU cc_start: 0.7708 (tt) cc_final: 0.7005 (mp) REVERT: B 395 LEU cc_start: 0.6306 (OUTLIER) cc_final: 0.5869 (pp) REVERT: B 563 TRP cc_start: 0.6706 (p-90) cc_final: 0.6460 (p-90) REVERT: B 630 ASP cc_start: 0.5867 (p0) cc_final: 0.5496 (m-30) outliers start: 30 outliers final: 22 residues processed: 121 average time/residue: 0.2253 time to fit residues: 38.3684 Evaluate side-chains 114 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR 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 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 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 589 SER Chi-restraints excluded: chain B residue 613 VAL 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: 2.9990 chunk 98 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.0570 chunk 62 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 116 optimal weight: 0.2980 chunk 95 optimal weight: 5.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- 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 = 0.4611 r_free = 0.4611 target = 0.202351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.170931 restraints weight = 16133.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.168438 restraints weight = 20896.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.169776 restraints weight = 19964.726| |-----------------------------------------------------------------------------| r_work (final): 0.4283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9592 Z= 0.249 Angle : 0.768 15.242 12956 Z= 0.389 Chirality : 0.047 0.256 1383 Planarity : 0.005 0.081 1722 Dihedral : 6.651 55.335 1321 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % Rotamer: Outliers : 3.05 % Allowed : 24.11 % 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 (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: -3.47 (0.22), residues: 1208 helix: -1.50 (0.33), residues: 232 sheet: -1.93 (0.33), residues: 241 loop : -2.83 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 470 HIS 0.007 0.001 HIS B 616 PHE 0.032 0.002 PHE B 644 TYR 0.019 0.002 TYR A 131 ARG 0.003 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 123 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 MET cc_start: 0.7404 (tmm) cc_final: 0.6474 (tmm) REVERT: B 67 GLU cc_start: 0.5547 (OUTLIER) cc_final: 0.3744 (mp0) REVERT: B 170 LEU cc_start: 0.7605 (tt) cc_final: 0.6821 (mp) REVERT: B 242 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7499 (mtmt) REVERT: B 395 LEU cc_start: 0.6271 (OUTLIER) cc_final: 0.5938 (pp) REVERT: B 563 TRP cc_start: 0.6851 (p-90) cc_final: 0.6536 (p-90) REVERT: B 630 ASP cc_start: 0.6150 (p0) cc_final: 0.5891 (m-30) outliers start: 30 outliers final: 24 residues processed: 117 average time/residue: 0.2370 time to fit residues: 38.9297 Evaluate side-chains 116 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR 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 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 120 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 242 LYS 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 519 VAL Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 613 VAL 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: 4.9990 chunk 100 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 50 optimal weight: 0.0070 chunk 48 optimal weight: 40.0000 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 = 0.4629 r_free = 0.4629 target = 0.203967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.169984 restraints weight = 15992.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.168598 restraints weight = 18435.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.170526 restraints weight = 17377.689| |-----------------------------------------------------------------------------| r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9592 Z= 0.205 Angle : 0.747 13.965 12956 Z= 0.378 Chirality : 0.046 0.250 1383 Planarity : 0.005 0.078 1722 Dihedral : 6.447 53.367 1321 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Rotamer: Outliers : 2.85 % Allowed : 24.52 % Favored : 72.63 % 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: -3.34 (0.23), residues: 1208 helix: -1.41 (0.33), residues: 239 sheet: -1.82 (0.34), residues: 227 loop : -2.76 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 563 HIS 0.007 0.001 HIS B 616 PHE 0.029 0.001 PHE B 644 TYR 0.015 0.001 TYR A 131 ARG 0.003 0.000 ARG A 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2817.84 seconds wall clock time: 52 minutes 3.51 seconds (3123.51 seconds total)