Starting phenix.real_space_refine on Sun Dec 29 00:34:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n88_24233/12_2024/7n88_24233.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n88_24233/12_2024/7n88_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_24233/12_2024/7n88_24233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n88_24233/12_2024/7n88_24233.map" model { file = "/net/cci-nas-00/data/ceres_data/7n88_24233/12_2024/7n88_24233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n88_24233/12_2024/7n88_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-5532/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: 4.44, per 1000 atoms: 0.47 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: 2.64 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: 1.21 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: 3.54 Time building geometry restraints manager: 2.93 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: 0.010 Normalize map: mean=0, sd=1: 9.880 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 21.280 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.300 ------------------------------------------------------------------------------- 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 : 1.054 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: 0.2887 time to fit residues: 39.9504 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 : 1.024 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 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 : 1.072 Fit side-chains REVERT: B 27 MET cc_start: 0.7335 (tpp) cc_final: 0.6839 (mtt) REVERT: B 67 GLU cc_start: 0.5642 (OUTLIER) cc_final: 0.3788 (mp0) REVERT: B 170 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6658 (tt) REVERT: B 395 LEU cc_start: 0.5848 (OUTLIER) cc_final: 0.5391 (pp) outliers start: 26 outliers final: 12 residues processed: 133 average time/residue: 0.2506 time to fit residues: 46.3497 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 : 1.041 ------------------------------------------------------------------------------- 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 61 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 30 optimal weight: 30.0000 chunk 110 optimal weight: 0.8980 chunk 118 optimal weight: 0.4980 chunk 98 optimal weight: 3.9990 chunk 109 optimal weight: 0.0270 chunk 37 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN B 330 GLN B 598 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 9592 Z= 0.242 Angle : 0.802 18.318 12956 Z= 0.415 Chirality : 0.047 0.286 1383 Planarity : 0.005 0.076 1722 Dihedral : 7.456 51.469 1325 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.24 % Favored : 85.76 % Rotamer: Outliers : 4.17 % Allowed : 17.50 % Favored : 78.33 % 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: -4.69 (0.20), residues: 1208 helix: -2.78 (0.27), residues: 238 sheet: -2.30 (0.33), residues: 219 loop : -3.70 (0.19), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 563 HIS 0.012 0.001 HIS B 598 PHE 0.013 0.002 PHE B 287 TYR 0.019 0.002 TYR B 66 ARG 0.002 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: 41 poor density : 101 time to evaluate : 1.159 Fit side-chains revert: symmetry clash REVERT: B 27 MET cc_start: 0.7260 (tpp) cc_final: 0.6813 (mtt) REVERT: B 67 GLU cc_start: 0.5486 (OUTLIER) cc_final: 0.3572 (mp0) REVERT: B 170 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.5975 (tt) REVERT: B 395 LEU cc_start: 0.6104 (OUTLIER) cc_final: 0.5555 (pp) REVERT: B 633 CYS cc_start: 0.5647 (m) cc_final: 0.5129 (p) outliers start: 41 outliers final: 23 residues processed: 134 average time/residue: 0.2140 time to fit residues: 41.5148 Evaluate side-chains 104 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 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 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 108 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 73 optimal weight: 0.0000 chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.5390 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9592 Z= 0.296 Angle : 0.792 12.186 12956 Z= 0.409 Chirality : 0.048 0.283 1383 Planarity : 0.006 0.081 1722 Dihedral : 7.434 51.012 1325 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.65 % Favored : 85.26 % Rotamer: Outliers : 4.17 % Allowed : 19.02 % Favored : 76.81 % 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: -2.55 (0.28), residues: 238 sheet: -2.35 (0.33), residues: 221 loop : -3.48 (0.19), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 563 HIS 0.008 0.001 HIS B 598 PHE 0.031 0.002 PHE B 644 TYR 0.024 0.002 TYR A 251 ARG 0.004 0.000 ARG B 603 *********************** 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 123 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 82 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: B 27 MET cc_start: 0.7188 (tpp) cc_final: 0.6785 (mtt) REVERT: B 37 CYS cc_start: 0.6455 (OUTLIER) cc_final: 0.6046 (m) REVERT: B 67 GLU cc_start: 0.5582 (OUTLIER) cc_final: 0.3712 (mp0) REVERT: B 395 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5820 (pp) REVERT: B 412 LEU cc_start: 0.5608 (OUTLIER) cc_final: 0.5347 (mm) REVERT: B 633 CYS cc_start: 0.5534 (m) cc_final: 0.5121 (p) outliers start: 41 outliers final: 23 residues processed: 117 average time/residue: 0.2074 time to fit residues: 35.0935 Evaluate side-chains 101 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 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 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 617 GLN Chi-restraints excluded: chain B residue 634 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 30.0000 chunk 99 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 30.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.143 9592 Z= 0.374 Angle : 0.839 17.506 12956 Z= 0.432 Chirality : 0.049 0.274 1383 Planarity : 0.006 0.081 1722 Dihedral : 7.662 60.386 1323 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 16.23 % Favored : 83.69 % Rotamer: Outliers : 5.09 % Allowed : 19.74 % 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: -4.37 (0.21), residues: 1208 helix: -2.44 (0.29), residues: 232 sheet: -2.28 (0.33), residues: 232 loop : -3.45 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 563 HIS 0.008 0.001 HIS A 299 PHE 0.021 0.002 PHE B 644 TYR 0.022 0.003 TYR A 251 ARG 0.003 0.000 ARG B 534 *********************** 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 135 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 85 time to evaluate : 1.110 Fit side-chains REVERT: B 27 MET cc_start: 0.7278 (tpp) cc_final: 0.6907 (mtt) REVERT: B 67 GLU cc_start: 0.5578 (OUTLIER) cc_final: 0.3674 (mp0) REVERT: B 395 LEU cc_start: 0.6319 (OUTLIER) cc_final: 0.5993 (pp) REVERT: B 412 LEU cc_start: 0.5740 (OUTLIER) cc_final: 0.5442 (mm) REVERT: B 594 MET cc_start: 0.4877 (mpp) cc_final: 0.4559 (mpp) REVERT: B 633 CYS cc_start: 0.5468 (m) cc_final: 0.5161 (p) outliers start: 50 outliers final: 33 residues processed: 126 average time/residue: 0.2030 time to fit residues: 37.2554 Evaluate side-chains 110 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 74 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 265 TYR 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 605 VAL Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.2980 chunk 112 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 616 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 9592 Z= 0.238 Angle : 0.772 17.289 12956 Z= 0.396 Chirality : 0.046 0.265 1383 Planarity : 0.005 0.079 1722 Dihedral : 7.047 51.631 1323 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.91 % Favored : 86.01 % Rotamer: Outliers : 4.58 % Allowed : 21.26 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.17 % Rama-Z (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: -4.21 (0.21), residues: 1208 helix: -2.33 (0.29), residues: 244 sheet: -2.28 (0.32), residues: 228 loop : -3.30 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 563 HIS 0.004 0.001 HIS B 598 PHE 0.019 0.001 PHE B 644 TYR 0.021 0.002 TYR A 251 ARG 0.004 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 139 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 94 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 205 TYR cc_start: 0.7189 (m-80) cc_final: 0.6971 (m-80) REVERT: B 27 MET cc_start: 0.7031 (tpp) cc_final: 0.6596 (mtt) REVERT: B 67 GLU cc_start: 0.5476 (OUTLIER) cc_final: 0.3601 (mp0) REVERT: B 343 ARG cc_start: 0.7640 (mpt180) cc_final: 0.7226 (mtt90) REVERT: B 395 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.5800 (pp) REVERT: B 412 LEU cc_start: 0.5441 (OUTLIER) cc_final: 0.5195 (mm) REVERT: B 594 MET cc_start: 0.4390 (mpp) cc_final: 0.4134 (mpp) REVERT: B 617 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8429 (pt0) REVERT: B 633 CYS cc_start: 0.5483 (m) cc_final: 0.5193 (p) REVERT: B 690 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7352 (mp) outliers start: 45 outliers final: 29 residues processed: 133 average time/residue: 0.2067 time to fit residues: 39.7813 Evaluate side-chains 115 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 81 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 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 526 ARG Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 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 566 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 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 13 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 9592 Z= 0.227 Angle : 0.767 14.610 12956 Z= 0.390 Chirality : 0.046 0.261 1383 Planarity : 0.005 0.079 1722 Dihedral : 6.871 50.213 1323 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 4.27 % Allowed : 22.18 % Favored : 73.55 % 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: -3.92 (0.22), residues: 1208 helix: -2.00 (0.31), residues: 231 sheet: -2.14 (0.33), residues: 240 loop : -3.13 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 563 HIS 0.008 0.001 HIS B 616 PHE 0.022 0.001 PHE A 237 TYR 0.021 0.002 TYR B 66 ARG 0.003 0.000 ARG B 211 *********************** 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: 42 poor density : 92 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.7091 (tpp) cc_final: 0.6530 (mtt) REVERT: B 67 GLU cc_start: 0.5370 (OUTLIER) cc_final: 0.3478 (mp0) REVERT: B 343 ARG cc_start: 0.7602 (mpt180) cc_final: 0.7169 (mtt90) REVERT: B 395 LEU cc_start: 0.6370 (OUTLIER) cc_final: 0.6008 (pp) REVERT: B 412 LEU cc_start: 0.5855 (OUTLIER) cc_final: 0.5580 (mm) REVERT: B 617 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8296 (pt0) outliers start: 42 outliers final: 31 residues processed: 126 average time/residue: 0.2002 time to fit residues: 37.0517 Evaluate side-chains 113 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 78 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 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 418 CYS 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 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 365 LEU Chi-restraints excluded: chain B residue 382 ILE 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 617 GLN Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 108 optimal weight: 0.0980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 9592 Z= 0.253 Angle : 0.790 17.387 12956 Z= 0.402 Chirality : 0.046 0.260 1383 Planarity : 0.005 0.079 1722 Dihedral : 6.882 51.555 1323 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.82 % Favored : 86.18 % Rotamer: Outliers : 4.98 % Allowed : 21.77 % Favored : 73.25 % 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: -3.82 (0.22), residues: 1208 helix: -1.88 (0.31), residues: 235 sheet: -2.10 (0.32), residues: 241 loop : -3.06 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 470 HIS 0.007 0.001 HIS B 616 PHE 0.020 0.002 PHE B 21 TYR 0.016 0.002 TYR A 251 ARG 0.003 0.000 ARG B 603 *********************** 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 143 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 94 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.7064 (tpp) cc_final: 0.6478 (mtt) REVERT: B 67 GLU cc_start: 0.5361 (OUTLIER) cc_final: 0.3586 (mp0) REVERT: B 343 ARG cc_start: 0.7546 (mpt180) cc_final: 0.7126 (mtt90) REVERT: B 395 LEU cc_start: 0.6103 (OUTLIER) cc_final: 0.5764 (pp) outliers start: 49 outliers final: 37 residues processed: 133 average time/residue: 0.2108 time to fit residues: 41.1589 Evaluate side-chains 120 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 81 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 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 526 ARG Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 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 617 GLN 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 111 optimal weight: 6.9990 chunk 65 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 0.0770 chunk 98 optimal weight: 0.0970 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.119 9592 Z= 0.209 Angle : 0.766 15.787 12956 Z= 0.391 Chirality : 0.045 0.294 1383 Planarity : 0.005 0.085 1722 Dihedral : 6.527 56.517 1323 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.00 % Favored : 87.00 % Rotamer: Outliers : 3.36 % Allowed : 24.11 % Favored : 72.53 % 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: -3.59 (0.23), residues: 1208 helix: -1.52 (0.33), residues: 233 sheet: -1.95 (0.34), residues: 227 loop : -2.97 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 563 HIS 0.006 0.001 HIS B 616 PHE 0.018 0.001 PHE B 644 TYR 0.015 0.001 TYR A 251 ARG 0.003 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 130 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 203 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7511 (pp) REVERT: A 413 MET cc_start: 0.7423 (tmm) cc_final: 0.6415 (tmm) REVERT: A 526 ARG cc_start: 0.2514 (OUTLIER) cc_final: 0.0158 (mmt90) REVERT: B 67 GLU cc_start: 0.5411 (OUTLIER) cc_final: 0.3856 (mp0) REVERT: B 343 ARG cc_start: 0.7545 (mpt180) cc_final: 0.7157 (mtt90) REVERT: B 395 LEU cc_start: 0.6064 (OUTLIER) cc_final: 0.5607 (pp) REVERT: B 617 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7374 (pt0) outliers start: 33 outliers final: 23 residues processed: 124 average time/residue: 0.2158 time to fit residues: 38.9090 Evaluate side-chains 115 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER 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 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 526 ARG Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 395 LEU 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 613 VAL Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 102 optimal weight: 0.0040 chunk 29 optimal weight: 5.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.250 9592 Z= 0.434 Angle : 0.921 34.431 12956 Z= 0.464 Chirality : 0.050 0.262 1383 Planarity : 0.006 0.096 1722 Dihedral : 7.198 58.458 1323 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.07 % Favored : 85.84 % Rotamer: Outliers : 3.87 % Allowed : 24.21 % Favored : 71.92 % 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: -3.71 (0.22), residues: 1208 helix: -1.80 (0.32), residues: 237 sheet: -1.99 (0.33), residues: 241 loop : -3.00 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 470 HIS 0.007 0.001 HIS A 299 PHE 0.030 0.002 PHE B 644 TYR 0.022 0.002 TYR A 162 ARG 0.005 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 125 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 87 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.7138 (tpp) cc_final: 0.6526 (mtt) REVERT: B 67 GLU cc_start: 0.5491 (OUTLIER) cc_final: 0.3814 (mp0) REVERT: B 343 ARG cc_start: 0.7639 (mpt180) cc_final: 0.7226 (mtt90) REVERT: B 395 LEU cc_start: 0.6261 (OUTLIER) cc_final: 0.5956 (pp) REVERT: B 617 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.7812 (pt0) outliers start: 38 outliers final: 33 residues processed: 115 average time/residue: 0.2039 time to fit residues: 34.1689 Evaluate side-chains 118 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 82 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 526 ARG Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 251 VAL 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 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 566 ASP Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 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 = 0.4625 r_free = 0.4625 target = 0.203351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.170801 restraints weight = 15858.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.168864 restraints weight = 22165.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.170769 restraints weight = 19499.685| |-----------------------------------------------------------------------------| r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.231 9592 Z= 0.314 Angle : 0.834 29.802 12956 Z= 0.417 Chirality : 0.046 0.246 1383 Planarity : 0.005 0.087 1722 Dihedral : 6.835 60.298 1323 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.91 % Favored : 87.00 % Rotamer: Outliers : 3.76 % Allowed : 24.01 % Favored : 72.23 % Cbeta Deviations : 0.09 % 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: -3.52 (0.23), residues: 1208 helix: -1.56 (0.33), residues: 235 sheet: -1.92 (0.33), residues: 241 loop : -2.89 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 563 HIS 0.006 0.001 HIS B 616 PHE 0.033 0.002 PHE B 644 TYR 0.015 0.001 TYR A 251 ARG 0.004 0.000 ARG A 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1973.28 seconds wall clock time: 37 minutes 34.75 seconds (2254.75 seconds total)