Starting phenix.real_space_refine on Mon May 26 01:32:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rmp_19366/05_2025/8rmp_19366.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rmp_19366/05_2025/8rmp_19366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rmp_19366/05_2025/8rmp_19366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rmp_19366/05_2025/8rmp_19366.map" model { file = "/net/cci-nas-00/data/ceres_data/8rmp_19366/05_2025/8rmp_19366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rmp_19366/05_2025/8rmp_19366.cif" } resolution = 2.77 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= 0.001 sd= 0.074 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: 6 Type Number sf(0) Gaussians Mg 1 5.21 5 S 103 5.16 5 C 8725 2.51 5 N 2397 2.21 5 O 2592 1.98 5 H 13813 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27631 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 11418 Classifications: {'peptide': 707} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 32, 'TRANS': 674} Chain breaks: 1 Chain: "B" Number of atoms: 11294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 11294 Classifications: {'peptide': 710} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 679} Chain breaks: 4 Chain: "C" Number of atoms: 4918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 4918 Classifications: {'peptide': 300} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 286} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.19, per 1000 atoms: 0.48 Number of scatterers: 27631 At special positions: 0 Unit cell: (112.56, 110.88, 137.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 103 16.00 Mg 1 11.99 O 2592 8.00 N 2397 7.00 C 8725 6.00 H 13813 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.33 Conformation dependent library (CDL) restraints added in 2.1 seconds 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 18 sheets defined 52.1% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 Processing helix chain 'A' and resid 10 through 24 removed outlier: 3.788A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 50 removed outlier: 3.600A pdb=" N PHE A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 185 Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.554A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 382 through 385 removed outlier: 4.035A pdb=" N LYS A 385 " --> pdb=" O GLU A 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 382 through 385' Processing helix chain 'A' and resid 404 through 415 removed outlier: 4.414A pdb=" N GLN A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 451 Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 529 through 538 Proline residue: A 534 - end of helix removed outlier: 3.768A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 582 through 604 removed outlier: 3.966A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 4.033A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 697 through 716 removed outlier: 3.789A pdb=" N ARG A 716 " --> pdb=" O THR A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.653A pdb=" N GLY B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 175 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.616A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 292 removed outlier: 4.079A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA B 280 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 345 removed outlier: 4.394A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.984A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE B 376 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 474 Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 687 through 694 Processing helix chain 'B' and resid 701 through 706 removed outlier: 4.214A pdb=" N TYR B 705 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 733 Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.771A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 27 through 33 removed outlier: 3.570A pdb=" N LYS C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 52 removed outlier: 3.801A pdb=" N ALA C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 removed outlier: 3.517A pdb=" N MET C 64 " --> pdb=" O LYS C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.576A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 115 removed outlier: 4.293A pdb=" N LYS C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 169 through 172 removed outlier: 3.882A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 183 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 701 through 705 Processing helix chain 'C' and resid 709 through 716 removed outlier: 4.497A pdb=" N SER C 714 " --> pdb=" O ASN C 711 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN C 715 " --> pdb=" O GLU C 712 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA3, first strand: chain 'A' and resid 195 through 196 removed outlier: 3.537A pdb=" N GLU A 199 " --> pdb=" O ARG A 196 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 258 through 259 removed outlier: 4.783A pdb=" N ASP B 305 " --> pdb=" O SER B 478 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N LYS B 480 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N THR B 303 " --> pdb=" O LYS B 480 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N SER B 482 " --> pdb=" O THR B 301 " (cutoff:3.500A) removed outlier: 11.271A pdb=" N THR B 301 " --> pdb=" O SER B 482 " (cutoff:3.500A) removed outlier: 10.446A pdb=" N ILE B 484 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 11.715A pdb=" N SER B 299 " --> pdb=" O ILE B 484 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 292 removed outlier: 7.175A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLY A 555 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG A 551 " --> pdb=" O GLY A 555 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL A 557 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU A 549 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 542 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLY A 546 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N GLU A 319 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N MET A 548 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 10.022A pdb=" N TRP A 317 " --> pdb=" O MET A 548 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 290 through 292 removed outlier: 5.376A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 377 through 380 removed outlier: 4.080A pdb=" N GLN B 367 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.264A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB2, first strand: chain 'B' and resid 178 through 182 Processing sheet with id=AB3, first strand: chain 'B' and resid 243 through 244 removed outlier: 6.920A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB5, first strand: chain 'B' and resid 642 through 643 Processing sheet with id=AB6, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.616A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 129 through 135 removed outlier: 4.339A pdb=" N MET C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 141 through 146 Processing sheet with id=AB9, first strand: chain 'C' and resid 694 through 699 removed outlier: 5.810A pdb=" N LEU C 733 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LYS C 699 " --> pdb=" O VAL C 731 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL C 731 " --> pdb=" O LYS C 699 " (cutoff:3.500A) 716 hydrogen bonds defined for protein. 1971 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: 10.19 Time building geometry restraints manager: 8.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13784 1.03 - 1.23: 40 1.23 - 1.42: 5784 1.42 - 1.62: 8118 1.62 - 1.81: 177 Bond restraints: 27903 Sorted by residual: bond pdb=" N ILE B 743 " pdb=" CA ILE B 743 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.74e+00 bond pdb=" N ARG B 734 " pdb=" H ARG B 734 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.43e+00 bond pdb=" N ILE B 735 " pdb=" CA ILE B 735 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.33e+00 bond pdb=" N SER B 732 " pdb=" H SER B 732 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.27e+00 bond pdb=" N ARG B 734 " pdb=" CA ARG B 734 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.22e-02 6.72e+03 7.04e+00 ... (remaining 27898 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 49510 1.47 - 2.94: 843 2.94 - 4.40: 90 4.40 - 5.87: 10 5.87 - 7.34: 3 Bond angle restraints: 50456 Sorted by residual: angle pdb=" C ARG B 734 " pdb=" N ILE B 735 " pdb=" CA ILE B 735 " ideal model delta sigma weight residual 121.97 129.31 -7.34 1.80e+00 3.09e-01 1.66e+01 angle pdb=" C MET B 744 " pdb=" N LYS B 745 " pdb=" CA LYS B 745 " ideal model delta sigma weight residual 120.29 125.94 -5.65 1.42e+00 4.96e-01 1.58e+01 angle pdb=" C LYS B 736 " pdb=" N LYS B 737 " pdb=" CA LYS B 737 " ideal model delta sigma weight residual 121.19 127.41 -6.22 1.59e+00 3.96e-01 1.53e+01 angle pdb=" C ALA B 741 " pdb=" N GLU B 742 " pdb=" CA GLU B 742 " ideal model delta sigma weight residual 120.44 125.24 -4.80 1.30e+00 5.92e-01 1.36e+01 angle pdb=" N ILE B 735 " pdb=" CA ILE B 735 " pdb=" C ILE B 735 " ideal model delta sigma weight residual 109.34 102.17 7.17 2.08e+00 2.31e-01 1.19e+01 ... (remaining 50451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 11377 17.65 - 35.31: 1120 35.31 - 52.96: 433 52.96 - 70.62: 104 70.62 - 88.27: 32 Dihedral angle restraints: 13066 sinusoidal: 7243 harmonic: 5823 Sorted by residual: dihedral pdb=" CA CYS B 693 " pdb=" C CYS B 693 " pdb=" N ASN B 694 " pdb=" CA ASN B 694 " ideal model delta harmonic sigma weight residual 180.00 162.68 17.32 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ARG B 602 " pdb=" C ARG B 602 " pdb=" N ASN B 603 " pdb=" CA ASN B 603 " ideal model delta harmonic sigma weight residual 180.00 -162.85 -17.15 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ASP A 286 " pdb=" CB ASP A 286 " pdb=" CG ASP A 286 " pdb=" OD1 ASP A 286 " ideal model delta sinusoidal sigma weight residual -30.00 -86.90 56.90 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 13063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1797 0.053 - 0.105: 232 0.105 - 0.158: 45 0.158 - 0.211: 0 0.211 - 0.263: 1 Chirality restraints: 2075 Sorted by residual: chirality pdb=" CA ILE B 735 " pdb=" N ILE B 735 " pdb=" C ILE B 735 " pdb=" CB ILE B 735 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB THR B 42 " pdb=" CA THR B 42 " pdb=" OG1 THR B 42 " pdb=" CG2 THR B 42 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILE B 667 " pdb=" N ILE B 667 " pdb=" C ILE B 667 " pdb=" CB ILE B 667 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 2072 not shown) Planarity restraints: 4079 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 730 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" C PHE B 730 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE B 730 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU B 731 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 181 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.91e+00 pdb=" CD GLU A 181 " 0.024 2.00e-02 2.50e+03 pdb=" OE1 GLU A 181 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU A 181 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 271 " 0.021 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO B 272 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " 0.015 5.00e-02 4.00e+02 ... (remaining 4076 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1553 2.18 - 2.79: 55311 2.79 - 3.39: 78195 3.39 - 4.00: 103695 4.00 - 4.60: 160882 Nonbonded interactions: 399636 Sorted by model distance: nonbonded pdb=" H GLY B 710 " pdb=" OD1 ASP C 26 " model vdw 1.576 2.450 nonbonded pdb=" OD2 ASP B 593 " pdb=" HH TYR B 620 " model vdw 1.592 2.450 nonbonded pdb=" HZ2 LYS A 506 " pdb=" OG SER A 509 " model vdw 1.613 2.450 nonbonded pdb=" O THR B 42 " pdb=" HG1 THR B 46 " model vdw 1.616 2.450 nonbonded pdb=" OE1 GLU B 575 " pdb=" HE ARG C 101 " model vdw 1.620 2.450 ... (remaining 399631 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 individual isotropic 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: 5.990 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: 0.530 Extract box with map and model: 1.210 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 56.950 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 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:10.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14090 Z= 0.142 Angle : 0.508 7.341 18989 Z= 0.286 Chirality : 0.038 0.263 2075 Planarity : 0.003 0.031 2446 Dihedral : 18.555 88.273 5402 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.94 % Favored : 97.00 % Rotamer: Outliers : 2.95 % Allowed : 23.43 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.18 (0.21), residues: 1699 helix: 2.04 (0.19), residues: 810 sheet: 0.80 (0.40), residues: 181 loop : -0.74 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 577 HIS 0.009 0.001 HIS A 128 PHE 0.012 0.001 PHE B 505 TYR 0.013 0.001 TYR B 555 ARG 0.003 0.000 ARG B 727 Details of bonding type rmsd hydrogen bonds : bond 0.12920 ( 712) hydrogen bonds : angle 5.26661 ( 1971) covalent geometry : bond 0.00280 (14090) covalent geometry : angle 0.50797 (18989) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 39 residues processed: 239 average time/residue: 2.3339 time to fit residues: 621.5204 Evaluate side-chains 225 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 186 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 210 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 155 optimal weight: 0.2980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN B 456 HIS B 549 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.152195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.120278 restraints weight = 50985.548| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.06 r_work: 0.3281 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.0626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14090 Z= 0.168 Angle : 0.513 4.795 18989 Z= 0.275 Chirality : 0.039 0.145 2075 Planarity : 0.004 0.032 2446 Dihedral : 6.946 55.432 1929 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.35 % Rotamer: Outliers : 3.73 % Allowed : 23.23 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.99 (0.20), residues: 1699 helix: 1.82 (0.18), residues: 819 sheet: 0.94 (0.41), residues: 169 loop : -0.82 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 309 HIS 0.007 0.001 HIS A 128 PHE 0.011 0.001 PHE B 551 TYR 0.013 0.001 TYR B 555 ARG 0.004 0.000 ARG B 393 Details of bonding type rmsd hydrogen bonds : bond 0.04883 ( 712) hydrogen bonds : angle 4.75958 ( 1971) covalent geometry : bond 0.00396 (14090) covalent geometry : angle 0.51265 (18989) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 195 time to evaluate : 2.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8215 (mm-40) REVERT: A 611 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7502 (m-80) REVERT: B 227 MET cc_start: 0.3798 (OUTLIER) cc_final: 0.3336 (ttt) REVERT: B 350 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6660 (mtt-85) outliers start: 57 outliers final: 26 residues processed: 232 average time/residue: 2.3064 time to fit residues: 597.7279 Evaluate side-chains 222 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 165 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 88 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.152518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.120046 restraints weight = 51160.033| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.12 r_work: 0.3279 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14090 Z= 0.144 Angle : 0.491 4.790 18989 Z= 0.262 Chirality : 0.038 0.144 2075 Planarity : 0.003 0.032 2446 Dihedral : 6.016 52.887 1901 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.65 % Rotamer: Outliers : 3.60 % Allowed : 23.89 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.93 (0.20), residues: 1699 helix: 1.79 (0.18), residues: 819 sheet: 0.90 (0.42), residues: 169 loop : -0.87 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 577 HIS 0.007 0.001 HIS A 128 PHE 0.011 0.001 PHE B 551 TYR 0.013 0.001 TYR B 555 ARG 0.002 0.000 ARG B 393 Details of bonding type rmsd hydrogen bonds : bond 0.04400 ( 712) hydrogen bonds : angle 4.63019 ( 1971) covalent geometry : bond 0.00336 (14090) covalent geometry : angle 0.49140 (18989) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 197 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 TYR cc_start: 0.8564 (m-80) cc_final: 0.8360 (m-80) REVERT: A 372 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.6225 (tp30) REVERT: A 481 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8264 (mm-40) REVERT: A 611 PHE cc_start: 0.7803 (OUTLIER) cc_final: 0.7548 (m-80) REVERT: B 227 MET cc_start: 0.3709 (OUTLIER) cc_final: 0.3273 (ttt) REVERT: B 277 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6862 (mt-10) REVERT: B 350 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6660 (mtt-85) REVERT: B 409 MET cc_start: 0.4615 (OUTLIER) cc_final: 0.4188 (mmm) outliers start: 55 outliers final: 25 residues processed: 234 average time/residue: 2.3352 time to fit residues: 609.7549 Evaluate side-chains 222 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 165 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 141 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.151188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.118688 restraints weight = 51442.778| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.12 r_work: 0.3258 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14090 Z= 0.173 Angle : 0.508 5.393 18989 Z= 0.271 Chirality : 0.039 0.147 2075 Planarity : 0.004 0.032 2446 Dihedral : 5.849 51.362 1898 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.19 % Allowed : 22.97 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.93 (0.21), residues: 1699 helix: 1.80 (0.18), residues: 807 sheet: 0.90 (0.41), residues: 175 loop : -0.84 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 577 HIS 0.007 0.001 HIS A 128 PHE 0.013 0.001 PHE B 505 TYR 0.014 0.001 TYR B 555 ARG 0.002 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.04470 ( 712) hydrogen bonds : angle 4.55254 ( 1971) covalent geometry : bond 0.00412 (14090) covalent geometry : angle 0.50792 (18989) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 195 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ILE cc_start: 0.7495 (mt) cc_final: 0.7188 (mt) REVERT: A 153 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7744 (mt-10) REVERT: A 181 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: A 372 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6354 (tp30) REVERT: A 481 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8219 (mm-40) REVERT: B 1 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.6600 (tmt) REVERT: B 227 MET cc_start: 0.3718 (OUTLIER) cc_final: 0.3315 (ttt) REVERT: B 277 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6593 (mp0) REVERT: B 287 ARG cc_start: 0.7188 (mtt180) cc_final: 0.6328 (mmt180) REVERT: B 350 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6712 (mtt-85) REVERT: B 409 MET cc_start: 0.4699 (OUTLIER) cc_final: 0.4281 (mmm) REVERT: C 1 MET cc_start: 0.7534 (ptp) cc_final: 0.7204 (ptt) outliers start: 64 outliers final: 28 residues processed: 237 average time/residue: 2.3956 time to fit residues: 631.3329 Evaluate side-chains 220 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 113 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN B 284 ASN B 314 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.152774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.120338 restraints weight = 51136.293| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.16 r_work: 0.3282 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14090 Z= 0.114 Angle : 0.477 5.011 18989 Z= 0.252 Chirality : 0.038 0.142 2075 Planarity : 0.003 0.033 2446 Dihedral : 5.531 52.668 1894 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.47 % Allowed : 23.69 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.03 (0.21), residues: 1699 helix: 1.91 (0.18), residues: 813 sheet: 0.96 (0.42), residues: 168 loop : -0.85 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 577 HIS 0.006 0.001 HIS A 128 PHE 0.014 0.001 PHE B 505 TYR 0.012 0.001 TYR B 555 ARG 0.002 0.000 ARG C 216 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 712) hydrogen bonds : angle 4.43205 ( 1971) covalent geometry : bond 0.00262 (14090) covalent geometry : angle 0.47717 (18989) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 189 time to evaluate : 2.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6279 (tp30) REVERT: A 481 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8209 (mm-40) REVERT: B 1 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.6447 (tmt) REVERT: B 113 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7791 (mp) REVERT: B 227 MET cc_start: 0.3714 (OUTLIER) cc_final: 0.3298 (ttt) REVERT: B 277 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6525 (mp0) REVERT: B 350 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6700 (mtt-85) REVERT: C 61 LYS cc_start: 0.7734 (tptp) cc_final: 0.7283 (pttm) outliers start: 53 outliers final: 27 residues processed: 222 average time/residue: 2.4164 time to fit residues: 596.8115 Evaluate side-chains 217 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 19 optimal weight: 1.9990 chunk 93 optimal weight: 0.0060 chunk 153 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 148 optimal weight: 0.0770 chunk 132 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 74 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN B 306 ASN B 314 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.153662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.120996 restraints weight = 51109.275| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.08 r_work: 0.3298 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14090 Z= 0.099 Angle : 0.470 5.185 18989 Z= 0.246 Chirality : 0.037 0.140 2075 Planarity : 0.003 0.032 2446 Dihedral : 5.373 53.639 1893 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.27 % Allowed : 24.35 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.15 (0.21), residues: 1699 helix: 2.04 (0.18), residues: 813 sheet: 0.97 (0.41), residues: 174 loop : -0.83 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 577 HIS 0.010 0.001 HIS A 128 PHE 0.011 0.001 PHE B 505 TYR 0.012 0.001 TYR B 555 ARG 0.004 0.000 ARG C 216 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 712) hydrogen bonds : angle 4.34018 ( 1971) covalent geometry : bond 0.00223 (14090) covalent geometry : angle 0.46964 (18989) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 191 time to evaluate : 2.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6223 (tp30) REVERT: A 481 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8249 (mm-40) REVERT: A 629 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8063 (mm-30) REVERT: B 1 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.6413 (tmt) REVERT: B 113 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7777 (mp) REVERT: B 277 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6503 (mp0) REVERT: B 350 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6608 (mtt-85) outliers start: 50 outliers final: 26 residues processed: 224 average time/residue: 2.3563 time to fit residues: 589.6858 Evaluate side-chains 216 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 210 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN B 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.151162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.118396 restraints weight = 51373.369| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.18 r_work: 0.3258 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14090 Z= 0.176 Angle : 0.506 5.088 18989 Z= 0.269 Chirality : 0.039 0.146 2075 Planarity : 0.004 0.033 2446 Dihedral : 5.216 53.171 1888 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.66 % Allowed : 24.08 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.94 (0.21), residues: 1699 helix: 1.86 (0.18), residues: 813 sheet: 0.74 (0.42), residues: 166 loop : -0.87 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 577 HIS 0.008 0.001 HIS A 128 PHE 0.014 0.001 PHE B 505 TYR 0.014 0.002 TYR B 555 ARG 0.004 0.000 ARG C 216 Details of bonding type rmsd hydrogen bonds : bond 0.04319 ( 712) hydrogen bonds : angle 4.41843 ( 1971) covalent geometry : bond 0.00420 (14090) covalent geometry : angle 0.50649 (18989) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 182 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6337 (tp30) REVERT: A 481 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8237 (mm-40) REVERT: B 1 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.6469 (tmt) REVERT: B 227 MET cc_start: 0.3713 (OUTLIER) cc_final: 0.3320 (ttt) REVERT: B 277 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6587 (mp0) REVERT: B 287 ARG cc_start: 0.7207 (mtt180) cc_final: 0.6357 (mmt180) REVERT: B 350 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6659 (mtt-85) outliers start: 56 outliers final: 33 residues processed: 219 average time/residue: 2.4642 time to fit residues: 598.6461 Evaluate side-chains 219 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 42 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 75 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 139 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN C 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.151636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.118714 restraints weight = 51236.160| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.08 r_work: 0.3267 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14090 Z= 0.136 Angle : 0.502 10.435 18989 Z= 0.263 Chirality : 0.038 0.143 2075 Planarity : 0.004 0.032 2446 Dihedral : 5.185 53.752 1888 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.95 % Allowed : 24.93 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.97 (0.21), residues: 1699 helix: 1.90 (0.18), residues: 811 sheet: 0.71 (0.42), residues: 166 loop : -0.86 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 577 HIS 0.007 0.001 HIS A 128 PHE 0.014 0.001 PHE B 505 TYR 0.013 0.001 TYR B 555 ARG 0.003 0.000 ARG B 260 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 712) hydrogen bonds : angle 4.41171 ( 1971) covalent geometry : bond 0.00321 (14090) covalent geometry : angle 0.50221 (18989) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 2.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: A 372 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6326 (tp30) REVERT: A 481 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8238 (mm-40) REVERT: B 1 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.6457 (tmt) REVERT: B 227 MET cc_start: 0.3725 (OUTLIER) cc_final: 0.3329 (ttt) REVERT: B 277 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6574 (mp0) REVERT: B 287 ARG cc_start: 0.7203 (mtt180) cc_final: 0.6340 (mmt180) REVERT: B 350 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6660 (mtt-85) outliers start: 45 outliers final: 30 residues processed: 215 average time/residue: 2.4410 time to fit residues: 583.0076 Evaluate side-chains 219 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 76 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN C 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.151406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.118851 restraints weight = 51234.819| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.13 r_work: 0.3262 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14090 Z= 0.154 Angle : 0.504 5.468 18989 Z= 0.267 Chirality : 0.038 0.144 2075 Planarity : 0.004 0.033 2446 Dihedral : 5.205 53.982 1888 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.01 % Allowed : 24.87 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.91 (0.21), residues: 1699 helix: 1.85 (0.18), residues: 811 sheet: 0.66 (0.42), residues: 166 loop : -0.87 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 577 HIS 0.007 0.001 HIS A 128 PHE 0.015 0.001 PHE B 505 TYR 0.013 0.001 TYR B 555 ARG 0.002 0.000 ARG B 260 Details of bonding type rmsd hydrogen bonds : bond 0.04236 ( 712) hydrogen bonds : angle 4.41355 ( 1971) covalent geometry : bond 0.00367 (14090) covalent geometry : angle 0.50409 (18989) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 182 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.5564 (tp30) cc_final: 0.5353 (tp30) REVERT: A 181 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.6734 (mp0) REVERT: A 372 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6305 (tp30) REVERT: A 481 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8244 (mm-40) REVERT: B 1 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.6469 (tmt) REVERT: B 227 MET cc_start: 0.3751 (OUTLIER) cc_final: 0.3340 (ttt) REVERT: B 277 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6533 (mp0) REVERT: B 287 ARG cc_start: 0.7222 (mtt180) cc_final: 0.6366 (mmt180) REVERT: B 350 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6659 (mtt-85) REVERT: B 744 MET cc_start: 0.7807 (mmp) cc_final: 0.7603 (mmp) outliers start: 46 outliers final: 30 residues processed: 217 average time/residue: 2.5014 time to fit residues: 603.8642 Evaluate side-chains 216 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 122 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.152567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.119752 restraints weight = 51328.851| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.10 r_work: 0.3276 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14090 Z= 0.121 Angle : 0.488 5.235 18989 Z= 0.258 Chirality : 0.038 0.140 2075 Planarity : 0.003 0.032 2446 Dihedral : 5.130 55.084 1888 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.55 % Allowed : 25.26 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.00 (0.21), residues: 1699 helix: 1.95 (0.18), residues: 811 sheet: 0.66 (0.42), residues: 166 loop : -0.86 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 577 HIS 0.006 0.001 HIS A 128 PHE 0.014 0.001 PHE B 505 TYR 0.012 0.001 TYR B 555 ARG 0.002 0.000 ARG B 260 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 712) hydrogen bonds : angle 4.35630 ( 1971) covalent geometry : bond 0.00283 (14090) covalent geometry : angle 0.48839 (18989) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.6660 (mp0) REVERT: A 372 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6344 (tp30) REVERT: A 481 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8232 (mm-40) REVERT: B 1 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.6461 (tmt) REVERT: B 227 MET cc_start: 0.3752 (OUTLIER) cc_final: 0.3302 (ttt) REVERT: B 277 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6510 (mp0) REVERT: B 287 ARG cc_start: 0.7209 (mtt180) cc_final: 0.6353 (mmt180) REVERT: B 350 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6641 (mtt-85) outliers start: 39 outliers final: 28 residues processed: 216 average time/residue: 2.4868 time to fit residues: 598.2130 Evaluate side-chains 216 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 136 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 123 optimal weight: 0.0870 chunk 66 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 168 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN B 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.152454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120289 restraints weight = 51327.354| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.18 r_work: 0.3280 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14090 Z= 0.125 Angle : 0.490 5.706 18989 Z= 0.258 Chirality : 0.038 0.154 2075 Planarity : 0.003 0.032 2446 Dihedral : 5.095 55.982 1888 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.62 % Allowed : 25.13 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.99 (0.21), residues: 1699 helix: 1.96 (0.18), residues: 811 sheet: 0.50 (0.41), residues: 171 loop : -0.85 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 577 HIS 0.007 0.001 HIS A 128 PHE 0.013 0.001 PHE B 505 TYR 0.013 0.001 TYR B 555 ARG 0.002 0.000 ARG B 260 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 712) hydrogen bonds : angle 4.33948 ( 1971) covalent geometry : bond 0.00296 (14090) covalent geometry : angle 0.49010 (18989) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19777.58 seconds wall clock time: 338 minutes 41.28 seconds (20321.28 seconds total)