Starting phenix.real_space_refine on Thu Jul 2 15:17:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vfi_31955/07_2026/7vfi_31955.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vfi_31955/07_2026/7vfi_31955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7vfi_31955/07_2026/7vfi_31955.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vfi_31955/07_2026/7vfi_31955.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vfi_31955/07_2026/7vfi_31955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vfi_31955/07_2026/7vfi_31955.map" model { file = "/net/cci-nas-00/data/ceres_data/7vfi_31955/07_2026/7vfi_31955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vfi_31955/07_2026/7vfi_31955.cif" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.042 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5719 2.51 5 N 1497 2.21 5 O 1651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8903 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4366 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 554} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 4361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4361 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 554} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 71 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.13, per 1000 atoms: 0.24 Number of scatterers: 8903 At special positions: 0 Unit cell: (68.89, 107.07, 136.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1651 8.00 N 1497 7.00 C 5719 6.00 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: 0.86 Conformation dependent library (CDL) restraints added in 329.7 milliseconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 6 sheets defined 68.1% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 180 through 214 Proline residue: A 202 - end of helix Processing helix chain 'A' and resid 218 through 266 removed outlier: 3.906A pdb=" N THR A 222 " --> pdb=" O MET A 218 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 removed outlier: 3.911A pdb=" N PHE A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 298 removed outlier: 3.827A pdb=" N LEU A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 321 Processing helix chain 'A' and resid 321 through 370 Proline residue: A 333 - end of helix removed outlier: 4.263A pdb=" N ALA A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.997A pdb=" N VAL A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 433 removed outlier: 4.570A pdb=" N LYS A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 480 removed outlier: 3.615A pdb=" N LEU A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N SER A 463 " --> pdb=" O GLY A 459 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LYS A 474 " --> pdb=" O GLY A 470 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE A 476 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N PHE A 478 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP A 480 " --> pdb=" O PHE A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 Processing helix chain 'A' and resid 570 through 578 Processing helix chain 'A' and resid 591 through 597 removed outlier: 4.198A pdb=" N SER A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 removed outlier: 3.532A pdb=" N VAL A 608 " --> pdb=" O PRO A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 623 Processing helix chain 'A' and resid 626 through 630 removed outlier: 3.795A pdb=" N SER A 629 " --> pdb=" O ASP A 626 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR A 630 " --> pdb=" O GLY A 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 626 through 630' Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 640 through 654 Processing helix chain 'A' and resid 672 through 679 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 730 through 737 Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 180 through 214 Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 217 through 267 removed outlier: 4.048A pdb=" N PHE B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 222 " --> pdb=" O MET B 218 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU B 230 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER B 267 " --> pdb=" O ARG B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 removed outlier: 4.062A pdb=" N PHE B 273 " --> pdb=" O GLU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 321 removed outlier: 5.191A pdb=" N ASP B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N THR B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ILE B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ASN B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 370 Proline residue: B 333 - end of helix removed outlier: 4.244A pdb=" N THR B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 removed outlier: 4.443A pdb=" N VAL B 374 " --> pdb=" O ALA B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 433 removed outlier: 3.907A pdb=" N LEU B 397 " --> pdb=" O GLN B 393 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 473 removed outlier: 3.689A pdb=" N LEU B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY B 464 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 549 Processing helix chain 'B' and resid 570 through 578 Processing helix chain 'B' and resid 591 through 597 Processing helix chain 'B' and resid 604 through 615 removed outlier: 4.088A pdb=" N VAL B 608 " --> pdb=" O PRO B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 640 through 654 Processing helix chain 'B' and resid 672 through 681 removed outlier: 3.628A pdb=" N LEU B 676 " --> pdb=" O GLU B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 700 removed outlier: 3.721A pdb=" N THR B 699 " --> pdb=" O ARG B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 726 removed outlier: 3.860A pdb=" N ALA B 725 " --> pdb=" O GLN B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 738 removed outlier: 3.716A pdb=" N MET B 738 " --> pdb=" O VAL B 734 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 524 through 525 removed outlier: 3.950A pdb=" N VAL A 500 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A 501 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 560 " --> pdb=" O ASP A 501 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 661 through 663 removed outlier: 6.705A pdb=" N THR A 531 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL A 708 " --> pdb=" O VAL A 715 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 516 through 521 removed outlier: 6.073A pdb=" N PHE B 507 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN B 519 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL B 505 " --> pdb=" O GLN B 519 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N VAL B 521 " --> pdb=" O GLU B 503 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU B 503 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASN B 504 " --> pdb=" O ARG B 558 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ARG B 558 " --> pdb=" O ASN B 504 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 506 " --> pdb=" O GLY B 556 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY B 556 " --> pdb=" O THR B 506 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 530 through 532 Processing sheet with id=AA5, first strand: chain 'B' and resid 560 through 561 Processing sheet with id=AA6, first strand: chain 'B' and resid 708 through 709 removed outlier: 7.046A pdb=" N VAL B 708 " --> pdb=" O VAL B 715 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1725 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2708 1.34 - 1.45: 1428 1.45 - 1.57: 4869 1.57 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 9069 Sorted by residual: bond pdb=" CAY Y01 A 801 " pdb=" OAG Y01 A 801 " ideal model delta sigma weight residual 1.207 1.431 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" CAY Y01 B 802 " pdb=" OAG Y01 B 802 " ideal model delta sigma weight residual 1.207 1.430 -0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" CAY Y01 B 801 " pdb=" OAG Y01 B 801 " ideal model delta sigma weight residual 1.207 1.430 -0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" CAI Y01 B 802 " pdb=" CAZ Y01 B 802 " ideal model delta sigma weight residual 1.332 1.528 -0.196 2.00e-02 2.50e+03 9.64e+01 bond pdb=" CAI Y01 A 801 " pdb=" CAZ Y01 A 801 " ideal model delta sigma weight residual 1.332 1.526 -0.194 2.00e-02 2.50e+03 9.39e+01 ... (remaining 9064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 12162 3.35 - 6.70: 129 6.70 - 10.05: 17 10.05 - 13.41: 5 13.41 - 16.76: 7 Bond angle restraints: 12320 Sorted by residual: angle pdb=" N GLU B 448 " pdb=" CA GLU B 448 " pdb=" C GLU B 448 " ideal model delta sigma weight residual 111.28 103.47 7.81 1.09e+00 8.42e-01 5.13e+01 angle pdb=" CAK Y01 B 801 " pdb=" CAI Y01 B 801 " pdb=" CAZ Y01 B 801 " ideal model delta sigma weight residual 124.96 108.20 16.76 3.00e+00 1.11e-01 3.12e+01 angle pdb=" CAM Y01 B 801 " pdb=" CAY Y01 B 801 " pdb=" OAG Y01 B 801 " ideal model delta sigma weight residual 125.42 108.67 16.75 3.00e+00 1.11e-01 3.12e+01 angle pdb=" CAM Y01 B 802 " pdb=" CAY Y01 B 802 " pdb=" OAG Y01 B 802 " ideal model delta sigma weight residual 125.42 108.75 16.67 3.00e+00 1.11e-01 3.09e+01 angle pdb=" CAK Y01 A 801 " pdb=" CAI Y01 A 801 " pdb=" CAZ Y01 A 801 " ideal model delta sigma weight residual 124.96 109.89 15.07 3.00e+00 1.11e-01 2.52e+01 ... (remaining 12315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 4745 17.13 - 34.26: 473 34.26 - 51.39: 116 51.39 - 68.52: 19 68.52 - 85.65: 13 Dihedral angle restraints: 5366 sinusoidal: 2052 harmonic: 3314 Sorted by residual: dihedral pdb=" CA PHE B 200 " pdb=" C PHE B 200 " pdb=" N LEU B 201 " pdb=" CA LEU B 201 " ideal model delta harmonic sigma weight residual -180.00 -151.40 -28.60 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA VAL A 228 " pdb=" C VAL A 228 " pdb=" N CYS A 229 " pdb=" CA CYS A 229 " ideal model delta harmonic sigma weight residual -180.00 -154.98 -25.02 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA MET A 218 " pdb=" C MET A 218 " pdb=" N ASP A 219 " pdb=" CA ASP A 219 " ideal model delta harmonic sigma weight residual 180.00 157.73 22.27 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 5363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1382 0.107 - 0.214: 78 0.214 - 0.321: 3 0.321 - 0.428: 0 0.428 - 0.535: 1 Chirality restraints: 1464 Sorted by residual: chirality pdb=" CBE Y01 B 802 " pdb=" CAP Y01 B 802 " pdb=" CBB Y01 B 802 " pdb=" CBI Y01 B 802 " both_signs ideal model delta sigma weight residual False 2.57 2.03 0.53 2.00e-01 2.50e+01 7.15e+00 chirality pdb=" CA ARG C 116 " pdb=" N ARG C 116 " pdb=" C ARG C 116 " pdb=" CB ARG C 116 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CBB Y01 B 802 " pdb=" CAC Y01 B 802 " pdb=" CAO Y01 B 802 " pdb=" CBE Y01 B 802 " both_signs ideal model delta sigma weight residual False 2.58 2.35 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1461 not shown) Planarity restraints: 1553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAM Y01 B 801 " 0.114 2.00e-02 2.50e+03 2.14e-01 4.57e+02 pdb=" CAY Y01 B 801 " -0.370 2.00e-02 2.50e+03 pdb=" OAG Y01 B 801 " 0.127 2.00e-02 2.50e+03 pdb=" OAW Y01 B 801 " 0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM Y01 B 802 " -0.116 2.00e-02 2.50e+03 2.12e-01 4.50e+02 pdb=" CAY Y01 B 802 " 0.367 2.00e-02 2.50e+03 pdb=" OAG Y01 B 802 " -0.124 2.00e-02 2.50e+03 pdb=" OAW Y01 B 802 " -0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM Y01 A 801 " 0.112 2.00e-02 2.50e+03 2.05e-01 4.20e+02 pdb=" CAY Y01 A 801 " -0.355 2.00e-02 2.50e+03 pdb=" OAG Y01 A 801 " 0.123 2.00e-02 2.50e+03 pdb=" OAW Y01 A 801 " 0.121 2.00e-02 2.50e+03 ... (remaining 1550 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1533 2.75 - 3.29: 9990 3.29 - 3.83: 15747 3.83 - 4.36: 17022 4.36 - 4.90: 27092 Nonbonded interactions: 71384 Sorted by model distance: nonbonded pdb=" O LEU B 561 " pdb=" OH TYR B 569 " model vdw 2.216 3.040 nonbonded pdb=" O LEU A 561 " pdb=" OH TYR A 569 " model vdw 2.220 3.040 nonbonded pdb=" O THR A 373 " pdb=" OG SER A 376 " model vdw 2.225 3.040 nonbonded pdb=" OG SER B 217 " pdb=" OD1 ASP B 219 " model vdw 2.260 3.040 nonbonded pdb=" O THR B 373 " pdb=" OG SER B 376 " model vdw 2.264 3.040 ... (remaining 71379 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 169 through 268 or (resid 269 and (name N or name CA or na \ me C or name O or name CB )) or resid 270 through 329 or (resid 330 and (name N \ or name CA or name C or name O or name CB )) or resid 331 through 669 or (resid \ 670 through 672 and (name N or name CA or name C or name O or name CB )) or resi \ d 673 through 677 or (resid 678 and (name N or name CA or name C or name O or na \ me CB )) or resid 679 through 683 or (resid 684 and (name N or name CA or name C \ or name O or name CB )) or resid 685 through 686 or (resid 687 and (name N or n \ ame CA or name C or name O or name CB )) or resid 688 through 695 or (resid 696 \ and (name N or name CA or name C or name O or name CB )) or resid 697 through 73 \ 5 or (resid 736 through 737 and (name N or name CA or name C or name O or name C \ B )) or resid 738 through 801)) selection = (chain 'B' and (resid 169 through 171 or (resid 172 and (name N or name CA or na \ me C or name O or name CB )) or resid 173 through 276 or (resid 277 and (name N \ or name CA or name C or name O or name CB )) or resid 278 through 335 or (resid \ 336 through 337 and (name N or name CA or name C or name O or name CB )) or resi \ d 338 through 634 or (resid 635 and (name N or name CA or name C or name O or na \ me CB )) or resid 636 through 645 or (resid 646 and (name N or name CA or name C \ or name O or name CB )) or resid 647 through 665 or (resid 666 through 672 and \ (name N or name CA or name C or name O or name CB )) or resid 673 through 734 or \ (resid 735 through 737 and (name N or name CA or name C or name O or name CB )) \ or resid 738 through 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.250 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.224 9069 Z= 0.408 Angle : 1.008 16.757 12320 Z= 0.518 Chirality : 0.055 0.535 1464 Planarity : 0.011 0.214 1553 Dihedral : 15.294 85.647 3240 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.21 % Allowed : 11.75 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.21), residues: 1143 helix: -1.02 (0.17), residues: 710 sheet: -4.19 (0.71), residues: 24 loop : -3.04 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 389 TYR 0.018 0.002 TYR B 395 PHE 0.019 0.002 PHE A 221 TRP 0.013 0.003 TRP B 410 HIS 0.009 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00819 / 0.41 ( 9069) covalent geometry : angle 1.00750 / 0.52 (12320) hydrogen bonds : bond 0.13997 / 9.54 ( 582) hydrogen bonds : angle 6.02321 / 4.47 ( 1725) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 ASP cc_start: 0.9182 (m-30) cc_final: 0.8976 (m-30) REVERT: A 352 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8959 (mt-10) REVERT: A 485 MET cc_start: 0.9474 (tpt) cc_final: 0.9269 (tmm) REVERT: A 598 TYR cc_start: 0.8904 (t80) cc_final: 0.8637 (t80) REVERT: A 610 GLU cc_start: 0.9870 (tt0) cc_final: 0.9620 (tp30) REVERT: B 260 CYS cc_start: 0.9551 (t) cc_final: 0.9326 (t) REVERT: B 336 MET cc_start: 0.9199 (mmt) cc_final: 0.8522 (tmm) REVERT: B 466 MET cc_start: 0.8930 (mmm) cc_final: 0.8451 (mmm) REVERT: B 576 ARG cc_start: 0.9452 (ttt-90) cc_final: 0.8557 (tpt90) outliers start: 2 outliers final: 2 residues processed: 153 average time/residue: 0.0686 time to fit residues: 16.2802 Evaluate side-chains 121 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 449 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 0.1980 chunk 53 optimal weight: 0.0570 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.8504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 GLN A 504 ASN A 520 ASN ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 ASN A 643 GLN A 645 GLN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN B 398 ASN B 519 GLN B 638 GLN ** B 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.052271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.039093 restraints weight = 50530.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.040631 restraints weight = 29226.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.041741 restraints weight = 20096.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.042578 restraints weight = 15268.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.043171 restraints weight = 12401.383| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9069 Z= 0.144 Angle : 0.644 9.205 12320 Z= 0.332 Chirality : 0.041 0.317 1464 Planarity : 0.004 0.046 1553 Dihedral : 6.346 59.965 1286 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.33 % Allowed : 16.51 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.24), residues: 1143 helix: 0.33 (0.18), residues: 748 sheet: -2.20 (0.66), residues: 44 loop : -2.77 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 256 TYR 0.016 0.001 TYR B 346 PHE 0.021 0.001 PHE A 190 TRP 0.007 0.001 TRP A 410 HIS 0.002 0.001 HIS B 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 9069) covalent geometry : angle 0.64366 / 0.33 (12320) hydrogen bonds : bond 0.05842 / 3.90 ( 582) hydrogen bonds : angle 4.79573 / 3.56 ( 1725) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 288 ASP cc_start: 0.9155 (m-30) cc_final: 0.8883 (m-30) REVERT: A 479 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9286 (mm) REVERT: A 598 TYR cc_start: 0.8704 (t80) cc_final: 0.8235 (t80) REVERT: A 649 MET cc_start: 0.9549 (tmm) cc_final: 0.9049 (ppp) REVERT: B 336 MET cc_start: 0.9137 (mmt) cc_final: 0.8495 (tmm) REVERT: B 466 MET cc_start: 0.8877 (mmm) cc_final: 0.8446 (mmm) REVERT: B 576 ARG cc_start: 0.9396 (ttt-90) cc_final: 0.8610 (tpt90) outliers start: 22 outliers final: 11 residues processed: 153 average time/residue: 0.0640 time to fit residues: 15.3183 Evaluate side-chains 126 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 662 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 42 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 88 optimal weight: 0.0050 chunk 57 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 HIS A 717 GLN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS B 688 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.053025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.039657 restraints weight = 49880.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.041230 restraints weight = 29295.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.042378 restraints weight = 20298.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.043235 restraints weight = 15482.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.043840 restraints weight = 12618.362| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9069 Z= 0.130 Angle : 0.641 11.466 12320 Z= 0.320 Chirality : 0.042 0.311 1464 Planarity : 0.003 0.051 1553 Dihedral : 5.972 57.556 1286 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.39 % Allowed : 18.94 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.25), residues: 1143 helix: 0.90 (0.19), residues: 746 sheet: -1.88 (0.69), residues: 44 loop : -2.56 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 258 TYR 0.015 0.001 TYR B 346 PHE 0.016 0.001 PHE A 190 TRP 0.006 0.001 TRP A 322 HIS 0.003 0.001 HIS A 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 ( 9069) covalent geometry : angle 0.64088 / 0.32 (12320) hydrogen bonds : bond 0.05284 / 3.49 ( 582) hydrogen bonds : angle 4.47725 / 3.32 ( 1725) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.235 Fit side-chains REVERT: A 288 ASP cc_start: 0.9086 (m-30) cc_final: 0.8814 (m-30) REVERT: A 296 VAL cc_start: 0.8974 (t) cc_final: 0.8755 (p) REVERT: A 479 ILE cc_start: 0.9480 (OUTLIER) cc_final: 0.9280 (mm) REVERT: A 598 TYR cc_start: 0.8708 (t80) cc_final: 0.8224 (t80) REVERT: A 610 GLU cc_start: 0.9853 (tt0) cc_final: 0.9624 (tp30) REVERT: B 291 MET cc_start: 0.9456 (ttt) cc_final: 0.8801 (tmm) REVERT: B 336 MET cc_start: 0.9142 (mmt) cc_final: 0.8468 (tmm) REVERT: B 416 LEU cc_start: 0.9656 (tp) cc_final: 0.9444 (pp) REVERT: B 466 MET cc_start: 0.8852 (mmm) cc_final: 0.8433 (mmm) REVERT: B 576 ARG cc_start: 0.9420 (ttt-90) cc_final: 0.8589 (tpt90) outliers start: 32 outliers final: 18 residues processed: 157 average time/residue: 0.0619 time to fit residues: 15.3652 Evaluate side-chains 142 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 454 CYS Chi-restraints excluded: chain B residue 632 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 108 optimal weight: 0.1980 chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 GLN B 268 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.052575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.039447 restraints weight = 50960.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.041006 restraints weight = 29806.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.042134 restraints weight = 20616.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.042982 restraints weight = 15689.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.043587 restraints weight = 12765.460| |-----------------------------------------------------------------------------| r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9069 Z= 0.134 Angle : 0.630 9.958 12320 Z= 0.316 Chirality : 0.041 0.308 1464 Planarity : 0.003 0.043 1553 Dihedral : 5.703 52.422 1284 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.28 % Allowed : 21.80 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.25), residues: 1143 helix: 1.19 (0.19), residues: 744 sheet: -1.70 (0.72), residues: 44 loop : -2.43 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 258 TYR 0.017 0.001 TYR A 346 PHE 0.013 0.001 PHE A 190 TRP 0.006 0.001 TRP B 322 HIS 0.003 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 9069) covalent geometry : angle 0.63031 / 0.32 (12320) hydrogen bonds : bond 0.05051 / 3.38 ( 582) hydrogen bonds : angle 4.42464 / 3.29 ( 1725) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 653 LEU cc_start: 0.9590 (tp) cc_final: 0.9197 (mm) REVERT: B 291 MET cc_start: 0.9494 (OUTLIER) cc_final: 0.8794 (tmm) REVERT: B 336 MET cc_start: 0.9138 (mmt) cc_final: 0.8481 (tmm) REVERT: B 382 GLU cc_start: 0.9490 (mp0) cc_final: 0.9085 (pm20) REVERT: B 416 LEU cc_start: 0.9658 (tp) cc_final: 0.9439 (pp) REVERT: B 466 MET cc_start: 0.8852 (mmm) cc_final: 0.8522 (mmm) REVERT: B 548 LEU cc_start: 0.9695 (OUTLIER) cc_final: 0.9348 (mm) REVERT: B 576 ARG cc_start: 0.9430 (ttt-90) cc_final: 0.8594 (tpt90) outliers start: 31 outliers final: 20 residues processed: 150 average time/residue: 0.0625 time to fit residues: 15.0329 Evaluate side-chains 146 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain B residue 454 CYS Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 632 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 87 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 90 optimal weight: 0.0060 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 overall best weight: 2.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.052221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.039023 restraints weight = 50633.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.040576 restraints weight = 29677.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.041709 restraints weight = 20566.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.042541 restraints weight = 15737.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.043142 restraints weight = 12825.404| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9069 Z= 0.148 Angle : 0.634 9.713 12320 Z= 0.321 Chirality : 0.041 0.305 1464 Planarity : 0.003 0.040 1553 Dihedral : 5.636 51.557 1284 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.60 % Allowed : 22.96 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.25), residues: 1143 helix: 1.23 (0.19), residues: 758 sheet: -1.54 (0.75), residues: 44 loop : -2.35 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 258 TYR 0.015 0.001 TYR A 346 PHE 0.012 0.001 PHE A 190 TRP 0.005 0.001 TRP B 322 HIS 0.004 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 ( 9069) covalent geometry : angle 0.63389 / 0.32 (12320) hydrogen bonds : bond 0.05030 / 3.35 ( 582) hydrogen bonds : angle 4.46486 / 3.31 ( 1725) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.355 Fit side-chains REVERT: A 288 ASP cc_start: 0.9033 (m-30) cc_final: 0.8833 (m-30) REVERT: A 607 MET cc_start: 0.9662 (ttt) cc_final: 0.9244 (tpt) REVERT: A 610 GLU cc_start: 0.9854 (tt0) cc_final: 0.9628 (tp30) REVERT: B 291 MET cc_start: 0.9490 (OUTLIER) cc_final: 0.8792 (tmm) REVERT: B 336 MET cc_start: 0.9134 (mmt) cc_final: 0.8482 (tmm) REVERT: B 382 GLU cc_start: 0.9492 (mp0) cc_final: 0.9145 (pm20) REVERT: B 416 LEU cc_start: 0.9647 (tp) cc_final: 0.9430 (pp) REVERT: B 465 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9152 (pp) REVERT: B 466 MET cc_start: 0.8838 (mmm) cc_final: 0.8303 (mmm) REVERT: B 485 MET cc_start: 0.9070 (mmt) cc_final: 0.8396 (mmm) REVERT: B 548 LEU cc_start: 0.9701 (OUTLIER) cc_final: 0.9359 (mm) REVERT: B 576 ARG cc_start: 0.9432 (ttt-90) cc_final: 0.8593 (tpt90) outliers start: 34 outliers final: 24 residues processed: 142 average time/residue: 0.0643 time to fit residues: 14.6238 Evaluate side-chains 145 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain B residue 454 CYS Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 65 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.052309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.039120 restraints weight = 50625.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.040622 restraints weight = 30034.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.041744 restraints weight = 21005.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.042562 restraints weight = 16073.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.043166 restraints weight = 13130.477| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9069 Z= 0.152 Angle : 0.645 11.213 12320 Z= 0.323 Chirality : 0.041 0.304 1464 Planarity : 0.003 0.042 1553 Dihedral : 5.559 51.671 1284 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.81 % Allowed : 24.66 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.25), residues: 1143 helix: 1.23 (0.19), residues: 760 sheet: -1.37 (0.76), residues: 44 loop : -2.24 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 277 TYR 0.015 0.001 TYR B 346 PHE 0.012 0.001 PHE A 190 TRP 0.005 0.001 TRP B 322 HIS 0.004 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 ( 9069) covalent geometry : angle 0.64468 / 0.32 (12320) hydrogen bonds : bond 0.04978 / 3.33 ( 582) hydrogen bonds : angle 4.45338 / 3.31 ( 1725) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 288 ASP cc_start: 0.9020 (m-30) cc_final: 0.8771 (m-30) REVERT: A 607 MET cc_start: 0.9656 (ttt) cc_final: 0.9243 (tpt) REVERT: A 610 GLU cc_start: 0.9848 (tt0) cc_final: 0.9622 (tp30) REVERT: B 291 MET cc_start: 0.9505 (OUTLIER) cc_final: 0.8805 (tmm) REVERT: B 336 MET cc_start: 0.9151 (mmt) cc_final: 0.8507 (tmm) REVERT: B 371 MET cc_start: 0.8778 (ppp) cc_final: 0.8474 (ppp) REVERT: B 382 GLU cc_start: 0.9488 (mp0) cc_final: 0.9133 (pm20) REVERT: B 416 LEU cc_start: 0.9667 (tp) cc_final: 0.9431 (pp) REVERT: B 466 MET cc_start: 0.8833 (mmm) cc_final: 0.8381 (mmm) REVERT: B 548 LEU cc_start: 0.9719 (OUTLIER) cc_final: 0.9371 (mm) REVERT: B 576 ARG cc_start: 0.9445 (ttt-90) cc_final: 0.8633 (tpt90) outliers start: 36 outliers final: 25 residues processed: 142 average time/residue: 0.0574 time to fit residues: 13.0350 Evaluate side-chains 147 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 679 GLN Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 632 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 31 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 72 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.053292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.039944 restraints weight = 50922.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.041540 restraints weight = 29767.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.042686 restraints weight = 20557.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.043449 restraints weight = 15722.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.044101 restraints weight = 13041.133| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9069 Z= 0.125 Angle : 0.653 10.859 12320 Z= 0.317 Chirality : 0.042 0.302 1464 Planarity : 0.003 0.045 1553 Dihedral : 5.426 51.833 1284 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.13 % Allowed : 24.02 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.25), residues: 1143 helix: 1.50 (0.19), residues: 748 sheet: -1.18 (0.77), residues: 44 loop : -2.09 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 242 TYR 0.016 0.001 TYR A 598 PHE 0.013 0.001 PHE A 620 TRP 0.006 0.001 TRP B 322 HIS 0.002 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 ( 9069) covalent geometry : angle 0.65318 / 0.32 (12320) hydrogen bonds : bond 0.04846 / 3.24 ( 582) hydrogen bonds : angle 4.29215 / 3.18 ( 1725) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 288 ASP cc_start: 0.9026 (m-30) cc_final: 0.8772 (m-30) REVERT: A 607 MET cc_start: 0.9658 (ttt) cc_final: 0.9244 (tpt) REVERT: A 610 GLU cc_start: 0.9856 (tt0) cc_final: 0.9626 (tp30) REVERT: A 653 LEU cc_start: 0.9536 (tp) cc_final: 0.9216 (mm) REVERT: B 288 ASP cc_start: 0.9098 (OUTLIER) cc_final: 0.8438 (t70) REVERT: B 291 MET cc_start: 0.9504 (ttt) cc_final: 0.8800 (tmm) REVERT: B 336 MET cc_start: 0.9140 (mmt) cc_final: 0.8502 (tmm) REVERT: B 382 GLU cc_start: 0.9456 (mp0) cc_final: 0.9092 (pm20) REVERT: B 416 LEU cc_start: 0.9643 (tp) cc_final: 0.9420 (pp) REVERT: B 466 MET cc_start: 0.8777 (mmm) cc_final: 0.8416 (mmm) REVERT: B 485 MET cc_start: 0.8951 (mmt) cc_final: 0.8254 (mmm) REVERT: B 548 LEU cc_start: 0.9702 (OUTLIER) cc_final: 0.9351 (mm) outliers start: 39 outliers final: 28 residues processed: 149 average time/residue: 0.0578 time to fit residues: 13.9922 Evaluate side-chains 154 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 679 GLN Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain B residue 454 CYS Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 112 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 GLN ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.052166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.039012 restraints weight = 51391.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.040547 restraints weight = 30222.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.041662 restraints weight = 21021.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.042472 restraints weight = 16102.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.043050 restraints weight = 13207.685| |-----------------------------------------------------------------------------| r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9069 Z= 0.166 Angle : 0.670 11.440 12320 Z= 0.333 Chirality : 0.042 0.298 1464 Planarity : 0.003 0.044 1553 Dihedral : 5.449 51.266 1284 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.49 % Allowed : 25.50 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.25), residues: 1143 helix: 1.47 (0.19), residues: 748 sheet: -1.16 (0.77), residues: 44 loop : -1.96 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 277 TYR 0.014 0.001 TYR A 598 PHE 0.011 0.002 PHE A 190 TRP 0.004 0.001 TRP B 322 HIS 0.005 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 ( 9069) covalent geometry : angle 0.67021 / 0.33 (12320) hydrogen bonds : bond 0.04909 / 3.31 ( 582) hydrogen bonds : angle 4.45060 / 3.30 ( 1725) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 288 ASP cc_start: 0.9026 (m-30) cc_final: 0.8738 (m-30) REVERT: A 607 MET cc_start: 0.9652 (ttt) cc_final: 0.9242 (tpt) REVERT: A 610 GLU cc_start: 0.9848 (tt0) cc_final: 0.9620 (tp30) REVERT: A 653 LEU cc_start: 0.9551 (tp) cc_final: 0.9178 (mm) REVERT: B 288 ASP cc_start: 0.9106 (OUTLIER) cc_final: 0.8311 (t70) REVERT: B 291 MET cc_start: 0.9516 (OUTLIER) cc_final: 0.8858 (tmm) REVERT: B 336 MET cc_start: 0.9142 (mmt) cc_final: 0.8506 (tmm) REVERT: B 416 LEU cc_start: 0.9655 (tp) cc_final: 0.9441 (pp) REVERT: B 466 MET cc_start: 0.8773 (mmm) cc_final: 0.8344 (mmm) outliers start: 33 outliers final: 26 residues processed: 142 average time/residue: 0.0556 time to fit residues: 12.9223 Evaluate side-chains 146 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 679 GLN Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 112 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.052698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.039445 restraints weight = 51632.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.040952 restraints weight = 30445.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.042059 restraints weight = 21229.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.042784 restraints weight = 16296.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.043398 restraints weight = 13557.169| |-----------------------------------------------------------------------------| r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9069 Z= 0.179 Angle : 0.694 10.757 12320 Z= 0.344 Chirality : 0.043 0.305 1464 Planarity : 0.003 0.044 1553 Dihedral : 5.506 52.511 1284 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.70 % Allowed : 26.14 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.25), residues: 1143 helix: 1.44 (0.19), residues: 748 sheet: -1.07 (0.78), residues: 44 loop : -1.88 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 277 TYR 0.018 0.001 TYR A 598 PHE 0.011 0.002 PHE A 190 TRP 0.004 0.001 TRP A 410 HIS 0.006 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.18 ( 9069) covalent geometry : angle 0.69388 / 0.34 (12320) hydrogen bonds : bond 0.05017 / 3.39 ( 582) hydrogen bonds : angle 4.49909 / 3.34 ( 1725) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 288 ASP cc_start: 0.9020 (m-30) cc_final: 0.8725 (m-30) REVERT: A 448 GLU cc_start: 0.9143 (tm-30) cc_final: 0.8917 (tm-30) REVERT: A 607 MET cc_start: 0.9660 (ttt) cc_final: 0.9251 (tpt) REVERT: A 610 GLU cc_start: 0.9856 (tt0) cc_final: 0.9631 (tp30) REVERT: A 653 LEU cc_start: 0.9542 (tp) cc_final: 0.9181 (mm) REVERT: B 288 ASP cc_start: 0.9116 (OUTLIER) cc_final: 0.8351 (t70) REVERT: B 291 MET cc_start: 0.9524 (OUTLIER) cc_final: 0.8860 (tmm) REVERT: B 336 MET cc_start: 0.9152 (mmt) cc_final: 0.8515 (tmm) REVERT: B 382 GLU cc_start: 0.9493 (mp0) cc_final: 0.9053 (pm20) REVERT: B 416 LEU cc_start: 0.9649 (tp) cc_final: 0.9440 (pp) REVERT: B 466 MET cc_start: 0.8790 (mmm) cc_final: 0.8383 (mmm) REVERT: B 548 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9377 (mm) REVERT: B 738 MET cc_start: 0.9185 (pmm) cc_final: 0.8790 (pmm) outliers start: 35 outliers final: 28 residues processed: 139 average time/residue: 0.0468 time to fit residues: 10.7736 Evaluate side-chains 150 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 679 GLN Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain B residue 454 CYS Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 3 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.051623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.038976 restraints weight = 50573.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.040507 restraints weight = 29208.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.041599 restraints weight = 20097.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.042329 restraints weight = 15284.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.042961 restraints weight = 12647.963| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9069 Z= 0.174 Angle : 0.702 11.247 12320 Z= 0.346 Chirality : 0.043 0.312 1464 Planarity : 0.003 0.044 1553 Dihedral : 5.539 54.159 1284 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.70 % Allowed : 26.14 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.25), residues: 1143 helix: 1.42 (0.19), residues: 748 sheet: -0.92 (0.80), residues: 44 loop : -1.90 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 277 TYR 0.018 0.001 TYR A 598 PHE 0.012 0.002 PHE A 190 TRP 0.003 0.001 TRP A 410 HIS 0.005 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 ( 9069) covalent geometry : angle 0.70216 / 0.35 (12320) hydrogen bonds : bond 0.05101 / 3.46 ( 582) hydrogen bonds : angle 4.49898 / 3.34 ( 1725) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 ASP cc_start: 0.9002 (m-30) cc_final: 0.8723 (m-30) REVERT: A 448 GLU cc_start: 0.9172 (tm-30) cc_final: 0.8914 (tm-30) REVERT: A 607 MET cc_start: 0.9651 (ttt) cc_final: 0.9234 (tpt) REVERT: A 610 GLU cc_start: 0.9842 (tt0) cc_final: 0.9621 (tp30) REVERT: B 288 ASP cc_start: 0.9100 (OUTLIER) cc_final: 0.8335 (t70) REVERT: B 291 MET cc_start: 0.9536 (OUTLIER) cc_final: 0.8886 (tmm) REVERT: B 336 MET cc_start: 0.9155 (mmt) cc_final: 0.8510 (tmm) REVERT: B 382 GLU cc_start: 0.9513 (mp0) cc_final: 0.9150 (pm20) REVERT: B 466 MET cc_start: 0.8785 (mmm) cc_final: 0.8336 (mmm) REVERT: B 485 MET cc_start: 0.8986 (mmt) cc_final: 0.8253 (mmm) REVERT: B 548 LEU cc_start: 0.9718 (OUTLIER) cc_final: 0.9380 (mm) REVERT: B 738 MET cc_start: 0.9206 (pmm) cc_final: 0.8829 (pmm) outliers start: 35 outliers final: 32 residues processed: 141 average time/residue: 0.0550 time to fit residues: 12.5960 Evaluate side-chains 154 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 679 GLN Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 39 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.052036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.039309 restraints weight = 49993.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.040851 restraints weight = 28934.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.041968 restraints weight = 19935.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.042717 restraints weight = 15158.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.043374 restraints weight = 12514.538| |-----------------------------------------------------------------------------| r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9069 Z= 0.152 Angle : 0.713 13.166 12320 Z= 0.346 Chirality : 0.043 0.323 1464 Planarity : 0.003 0.044 1553 Dihedral : 5.505 54.233 1284 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.60 % Allowed : 26.77 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.25), residues: 1143 helix: 1.44 (0.19), residues: 748 sheet: -0.76 (0.82), residues: 44 loop : -1.90 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 277 TYR 0.018 0.001 TYR A 598 PHE 0.015 0.001 PHE A 318 TRP 0.004 0.001 TRP B 322 HIS 0.004 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 9069) covalent geometry : angle 0.71313 / 0.35 (12320) hydrogen bonds : bond 0.05064 / 3.43 ( 582) hydrogen bonds : angle 4.45673 / 3.30 ( 1725) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1358.11 seconds wall clock time: 24 minutes 18.30 seconds (1458.30 seconds total)