Starting phenix.real_space_refine on Fri Jul 3 03:15:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qdq_53032/07_2026/9qdq_53032.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qdq_53032/07_2026/9qdq_53032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qdq_53032/07_2026/9qdq_53032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qdq_53032/07_2026/9qdq_53032.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qdq_53032/07_2026/9qdq_53032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qdq_53032/07_2026/9qdq_53032.map" } resolution = 3.6 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= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 49 5.16 5 C 7231 2.51 5 N 1942 2.21 5 O 2151 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 11382 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6299 Classifications: {'peptide': 797} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 759} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 4494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4494 Classifications: {'peptide': 558} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 18, 'TRANS': 539} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'RNA': 9} Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 7} Link IDs: {'rna2p': 2, 'rna3p': 6} Time building chain proxies: 1.86, per 1000 atoms: 0.16 Number of scatterers: 11382 At special positions: 0 Unit cell: (91.9296, 107.251, 160.877, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 9 15.00 O 2151 8.00 N 1942 7.00 C 7231 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: 0.93 Conformation dependent library (CDL) restraints added in 523.4 milliseconds 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2672 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 8 sheets defined 55.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 93 through 102 Processing helix chain 'A' and resid 161 through 165 removed outlier: 4.009A pdb=" N GLN A 164 " --> pdb=" O ASP A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 190 Processing helix chain 'A' and resid 194 through 203 Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.629A pdb=" N ILE A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP A 217 " --> pdb=" O ILE A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 217' Processing helix chain 'A' and resid 234 through 259 Proline residue: A 244 - end of helix Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 355 through 371 removed outlier: 3.936A pdb=" N MET A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 375 removed outlier: 4.139A pdb=" N ILE A 375 " --> pdb=" O LYS A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 376 through 384 Processing helix chain 'A' and resid 410 through 421 removed outlier: 3.792A pdb=" N LEU A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 452 removed outlier: 3.977A pdb=" N THR A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 475 Processing helix chain 'A' and resid 494 through 497 Processing helix chain 'A' and resid 498 through 506 Processing helix chain 'A' and resid 509 through 522 removed outlier: 3.639A pdb=" N ASN A 513 " --> pdb=" O GLY A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 547 Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 573 through 577 Processing helix chain 'A' and resid 578 through 584 Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 619 through 628 Processing helix chain 'A' and resid 641 through 653 removed outlier: 4.846A pdb=" N PHE A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) Proline residue: A 648 - end of helix Processing helix chain 'A' and resid 702 through 719 Processing helix chain 'A' and resid 722 through 724 No H-bonds generated for 'chain 'A' and resid 722 through 724' Processing helix chain 'A' and resid 732 through 746 Processing helix chain 'A' and resid 750 through 756 removed outlier: 3.737A pdb=" N TYR A 754 " --> pdb=" O ASP A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 766 removed outlier: 3.765A pdb=" N GLN A 766 " --> pdb=" O ASP A 763 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 763 through 766' Processing helix chain 'A' and resid 787 through 790 removed outlier: 3.979A pdb=" N ARG A 790 " --> pdb=" O GLY A 787 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 787 through 790' Processing helix chain 'A' and resid 791 through 800 removed outlier: 3.982A pdb=" N LEU A 795 " --> pdb=" O ASP A 791 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR A 800 " --> pdb=" O ASN A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 816 removed outlier: 3.677A pdb=" N LEU A 815 " --> pdb=" O ASN A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 831 removed outlier: 3.548A pdb=" N LYS A 831 " --> pdb=" O HIS A 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 29 Processing helix chain 'B' and resid 30 through 33 Processing helix chain 'B' and resid 34 through 63 removed outlier: 4.104A pdb=" N LEU B 38 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 72 Processing helix chain 'B' and resid 74 through 88 removed outlier: 4.420A pdb=" N SER B 78 " --> pdb=" O GLN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 105 Processing helix chain 'B' and resid 111 through 148 removed outlier: 3.776A pdb=" N LYS B 115 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR B 148 " --> pdb=" O VAL B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 187 through 215 removed outlier: 4.001A pdb=" N LEU B 191 " --> pdb=" O PRO B 187 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Proline residue: B 193 - end of helix removed outlier: 3.511A pdb=" N GLU B 215 " --> pdb=" O THR B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 224 Processing helix chain 'B' and resid 225 through 239 Processing helix chain 'B' and resid 242 through 256 removed outlier: 4.092A pdb=" N TYR B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 276 through 288 Processing helix chain 'B' and resid 292 through 312 Processing helix chain 'B' and resid 316 through 334 removed outlier: 3.875A pdb=" N PHE B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 removed outlier: 4.201A pdb=" N TRP B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 368 Processing helix chain 'B' and resid 371 through 393 removed outlier: 3.984A pdb=" N PHE B 386 " --> pdb=" O THR B 382 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N HIS B 387 " --> pdb=" O ILE B 383 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 426 Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 438 through 454 removed outlier: 3.969A pdb=" N VAL B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN B 454 " --> pdb=" O TRP B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 463 removed outlier: 3.777A pdb=" N SER B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 482 Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 521 through 528 removed outlier: 3.645A pdb=" N MET B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 536 Processing helix chain 'B' and resid 540 through 544 Processing helix chain 'B' and resid 546 through 567 Processing helix chain 'C' and resid 170 through 186 Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 83 removed outlier: 3.595A pdb=" N LYS A 81 " --> pdb=" O CYS A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 148 removed outlier: 3.565A pdb=" N PHE A 135 " --> pdb=" O GLN A 166 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 166 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA4, first strand: chain 'A' and resid 262 through 271 removed outlier: 4.593A pdb=" N SER A 266 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N HIS A 277 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR A 329 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 303 " --> pdb=" O TRP A 311 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A 315 " --> pdb=" O MET A 299 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE A 347 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 393 removed outlier: 3.723A pdb=" N THR C 200 " --> pdb=" O SER A 392 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 479 through 481 removed outlier: 6.493A pdb=" N VAL A 480 " --> pdb=" O CYS A 551 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE A 455 " --> pdb=" O VAL A 550 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL A 569 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N VAL A 596 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE A 571 " --> pdb=" O VAL A 596 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU A 427 " --> pdb=" O ILE A 632 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 636 through 637 Processing sheet with id=AA8, first strand: chain 'A' and resid 758 through 761 removed outlier: 7.339A pdb=" N ILE A 726 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N ALA A 760 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL A 728 " --> pdb=" O ALA A 760 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER A 776 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASP A 771 " --> pdb=" O LYS A 803 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 773 " --> pdb=" O GLY A 805 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 807 " --> pdb=" O ILE A 773 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A 683 " --> pdb=" O LEU A 806 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY A 810 " --> pdb=" O TRP A 685 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL A 835 " --> pdb=" O MET A 682 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N PHE A 684 " --> pdb=" O VAL A 835 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1596 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: 1.79 Time building geometry restraints manager: 1.24 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: 3582 1.34 - 1.46: 1709 1.46 - 1.58: 6250 1.58 - 1.69: 17 1.69 - 1.81: 75 Bond restraints: 11633 Sorted by residual: bond pdb=" CG LYS A 512 " pdb=" CD LYS A 512 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.17e+00 bond pdb=" CB TRP B 450 " pdb=" CG TRP B 450 " ideal model delta sigma weight residual 1.498 1.459 0.039 3.10e-02 1.04e+03 1.62e+00 bond pdb=" CB LEU B 360 " pdb=" CG LEU B 360 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.54e+00 bond pdb=" N PRO B 275 " pdb=" CA PRO B 275 " ideal model delta sigma weight residual 1.467 1.452 0.015 1.19e-02 7.06e+03 1.53e+00 bond pdb=" CB ASN A 60 " pdb=" CG ASN A 60 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.29e+00 ... (remaining 11628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 15420 2.11 - 4.21: 258 4.21 - 6.32: 63 6.32 - 8.42: 22 8.42 - 10.53: 10 Bond angle restraints: 15773 Sorted by residual: angle pdb=" C ILE B 302 " pdb=" N MET B 303 " pdb=" CA MET B 303 " ideal model delta sigma weight residual 121.14 112.86 8.28 1.75e+00 3.27e-01 2.24e+01 angle pdb=" C MET B 270 " pdb=" N MET B 271 " pdb=" CA MET B 271 " ideal model delta sigma weight residual 122.56 114.76 7.80 1.72e+00 3.38e-01 2.06e+01 angle pdb=" N PRO B 275 " pdb=" CA PRO B 275 " pdb=" C PRO B 275 " ideal model delta sigma weight residual 111.32 118.04 -6.72 1.71e+00 3.42e-01 1.54e+01 angle pdb=" CA MET B 303 " pdb=" CB MET B 303 " pdb=" CG MET B 303 " ideal model delta sigma weight residual 114.10 121.74 -7.64 2.00e+00 2.50e-01 1.46e+01 angle pdb=" CA MET B 126 " pdb=" CB MET B 126 " pdb=" CG MET B 126 " ideal model delta sigma weight residual 114.10 121.45 -7.35 2.00e+00 2.50e-01 1.35e+01 ... (remaining 15768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6231 17.98 - 35.97: 662 35.97 - 53.95: 148 53.95 - 71.94: 31 71.94 - 89.92: 6 Dihedral angle restraints: 7078 sinusoidal: 2959 harmonic: 4119 Sorted by residual: dihedral pdb=" CA MET B 528 " pdb=" C MET B 528 " pdb=" N ASP B 529 " pdb=" CA ASP B 529 " ideal model delta harmonic sigma weight residual -180.00 -155.23 -24.77 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA LEU A 842 " pdb=" C LEU A 842 " pdb=" N GLN A 843 " pdb=" CA GLN A 843 " ideal model delta harmonic sigma weight residual 180.00 159.48 20.52 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA LEU A 634 " pdb=" C LEU A 634 " pdb=" N GLU A 635 " pdb=" CA GLU A 635 " ideal model delta harmonic sigma weight residual -180.00 -162.55 -17.45 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 7075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1542 0.064 - 0.129: 226 0.129 - 0.193: 13 0.193 - 0.257: 0 0.257 - 0.322: 3 Chirality restraints: 1784 Sorted by residual: chirality pdb=" CG LEU B 360 " pdb=" CB LEU B 360 " pdb=" CD1 LEU B 360 " pdb=" CD2 LEU B 360 " both_signs ideal model delta sigma weight residual False -2.59 -2.91 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CG LEU B 552 " pdb=" CB LEU B 552 " pdb=" CD1 LEU B 552 " pdb=" CD2 LEU B 552 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA PRO B 275 " pdb=" N PRO B 275 " pdb=" C PRO B 275 " pdb=" CB PRO B 275 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1781 not shown) Planarity restraints: 1984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 266 " 0.020 2.00e-02 2.50e+03 2.31e-02 9.34e+00 pdb=" CG PHE B 266 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE B 266 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 266 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B 266 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 266 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 266 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 431 " -0.020 2.00e-02 2.50e+03 1.91e-02 9.11e+00 pdb=" CG TRP B 431 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP B 431 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP B 431 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 431 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 431 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 431 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 431 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 431 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 431 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 165 " -0.017 2.00e-02 2.50e+03 1.58e-02 6.28e+00 pdb=" CG TRP A 165 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 165 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 165 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 165 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 165 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 165 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 165 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 165 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 165 " 0.001 2.00e-02 2.50e+03 ... (remaining 1981 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2799 2.79 - 3.32: 11428 3.32 - 3.84: 19047 3.84 - 4.37: 21808 4.37 - 4.90: 35993 Nonbonded interactions: 91075 Sorted by model distance: nonbonded pdb=" OD1 ASN B 413 " pdb=" OH TYR B 460 " model vdw 2.262 3.040 nonbonded pdb=" O ILE B 261 " pdb=" ND2 ASN B 265 " model vdw 2.264 3.120 nonbonded pdb=" O ASN A 746 " pdb=" ND2 ASN A 746 " model vdw 2.282 3.120 nonbonded pdb=" O ILE B 426 " pdb=" OG SER B 430 " model vdw 2.301 3.040 nonbonded pdb=" ND2 ASN A 781 " pdb=" O ALA A 785 " model vdw 2.309 3.120 ... (remaining 91070 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.710 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.420 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5944 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11633 Z= 0.146 Angle : 0.752 10.530 15773 Z= 0.381 Chirality : 0.045 0.322 1784 Planarity : 0.005 0.069 1984 Dihedral : 15.454 89.921 4406 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.40 % Allowed : 23.02 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.78 (0.23), residues: 1399 helix: 0.84 (0.20), residues: 691 sheet: 0.36 (0.53), residues: 107 loop : 0.36 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 531 TYR 0.022 0.001 TYR B 207 PHE 0.054 0.002 PHE B 266 TRP 0.051 0.003 TRP B 431 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (11633) covalent geometry : angle 0.75218 / 0.38 (15773) hydrogen bonds : bond 0.16970 / 11.33 ( 552) hydrogen bonds : angle 6.59891 / 4.70 ( 1596) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 743 MET cc_start: 0.6896 (mmt) cc_final: 0.6537 (mmt) REVERT: A 849 LEU cc_start: 0.8540 (pt) cc_final: 0.8083 (mt) REVERT: B 22 LEU cc_start: 0.7204 (tp) cc_final: 0.6915 (tp) REVERT: B 443 MET cc_start: 0.7495 (ppp) cc_final: 0.7115 (ppp) outliers start: 5 outliers final: 4 residues processed: 107 average time/residue: 0.0938 time to fit residues: 15.2001 Evaluate side-chains 94 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain B residue 487 PHE Chi-restraints excluded: chain C residue 181 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN A 422 GLN ** A 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN ** B 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 448 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.134461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.106491 restraints weight = 46869.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.109483 restraints weight = 26312.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.111614 restraints weight = 18370.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.112702 restraints weight = 14536.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.113716 restraints weight = 12615.398| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5960 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11633 Z= 0.141 Angle : 0.620 8.286 15773 Z= 0.322 Chirality : 0.042 0.186 1784 Planarity : 0.004 0.042 1984 Dihedral : 8.766 73.842 1663 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.09 % Allowed : 19.73 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.90 (0.23), residues: 1399 helix: 1.01 (0.20), residues: 692 sheet: -0.02 (0.47), residues: 125 loop : 0.42 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 537 TYR 0.017 0.001 TYR B 207 PHE 0.035 0.002 PHE B 266 TRP 0.021 0.002 TRP B 431 HIS 0.004 0.001 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (11633) covalent geometry : angle 0.61999 / 0.32 (15773) hydrogen bonds : bond 0.04744 / 3.20 ( 552) hydrogen bonds : angle 5.25941 / 3.72 ( 1596) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 743 MET cc_start: 0.7030 (mmt) cc_final: 0.6547 (mmt) REVERT: A 849 LEU cc_start: 0.8554 (pt) cc_final: 0.8040 (mt) REVERT: B 270 MET cc_start: 0.5998 (ptp) cc_final: 0.5796 (ptp) REVERT: B 274 MET cc_start: 0.7528 (tmm) cc_final: 0.6601 (mmp) REVERT: B 377 HIS cc_start: 0.7899 (m170) cc_final: 0.7686 (m90) outliers start: 26 outliers final: 14 residues processed: 115 average time/residue: 0.0768 time to fit residues: 14.0457 Evaluate side-chains 101 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 827 HIS Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 360 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 34 optimal weight: 0.0020 chunk 135 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 106 optimal weight: 7.9990 chunk 115 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 26 optimal weight: 0.1980 chunk 113 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN A 181 GLN A 796 ASN B 101 ASN B 421 HIS C 201 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.129435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.102384 restraints weight = 52280.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.105358 restraints weight = 28729.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.106989 restraints weight = 19780.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.108557 restraints weight = 15742.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.109129 restraints weight = 13408.994| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11633 Z= 0.139 Angle : 0.591 10.524 15773 Z= 0.303 Chirality : 0.042 0.225 1784 Planarity : 0.004 0.054 1984 Dihedral : 8.291 66.270 1653 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.29 % Allowed : 17.48 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.88 (0.23), residues: 1399 helix: 1.02 (0.20), residues: 691 sheet: -0.38 (0.45), residues: 123 loop : 0.47 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 537 TYR 0.021 0.002 TYR A 252 PHE 0.024 0.002 PHE B 266 TRP 0.025 0.002 TRP B 431 HIS 0.004 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (11633) covalent geometry : angle 0.59091 / 0.30 (15773) hydrogen bonds : bond 0.04274 / 2.88 ( 552) hydrogen bonds : angle 4.88916 / 3.44 ( 1596) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 101 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 698 THR cc_start: 0.7912 (OUTLIER) cc_final: 0.7610 (t) REVERT: A 743 MET cc_start: 0.7193 (mmt) cc_final: 0.6731 (mmt) REVERT: A 827 HIS cc_start: 0.7146 (OUTLIER) cc_final: 0.6075 (t-90) REVERT: A 849 LEU cc_start: 0.8570 (pt) cc_final: 0.8061 (mt) REVERT: B 99 TRP cc_start: 0.8064 (t60) cc_final: 0.7669 (t60) REVERT: B 101 ASN cc_start: 0.8749 (m110) cc_final: 0.8514 (p0) REVERT: B 274 MET cc_start: 0.7758 (tmm) cc_final: 0.7020 (mmp) outliers start: 41 outliers final: 17 residues processed: 131 average time/residue: 0.0725 time to fit residues: 14.9020 Evaluate side-chains 105 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 827 HIS Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 360 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 73 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN A 181 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.125839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.098964 restraints weight = 52757.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.101503 restraints weight = 29170.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.103354 restraints weight = 20371.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.104541 restraints weight = 16160.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.105056 restraints weight = 13967.236| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 11633 Z= 0.189 Angle : 0.658 10.717 15773 Z= 0.340 Chirality : 0.043 0.187 1784 Planarity : 0.005 0.070 1984 Dihedral : 8.585 67.859 1653 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.97 % Allowed : 19.01 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.63 (0.23), residues: 1399 helix: 0.82 (0.20), residues: 692 sheet: -0.69 (0.46), residues: 118 loop : 0.38 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 793 TYR 0.018 0.002 TYR A 238 PHE 0.021 0.002 PHE B 264 TRP 0.017 0.002 TRP A 353 HIS 0.005 0.001 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (11633) covalent geometry : angle 0.65845 / 0.34 (15773) hydrogen bonds : bond 0.04431 / 2.98 ( 552) hydrogen bonds : angle 5.04318 / 3.55 ( 1596) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.6257 (OUTLIER) cc_final: 0.5988 (t0) REVERT: A 827 HIS cc_start: 0.7298 (OUTLIER) cc_final: 0.6212 (t-90) REVERT: A 849 LEU cc_start: 0.8779 (pt) cc_final: 0.8204 (mt) REVERT: B 98 MET cc_start: 0.8218 (ttt) cc_final: 0.7614 (tpp) REVERT: B 101 ASN cc_start: 0.8816 (m110) cc_final: 0.8609 (m110) REVERT: B 274 MET cc_start: 0.7925 (tmm) cc_final: 0.7033 (mmm) outliers start: 37 outliers final: 20 residues processed: 118 average time/residue: 0.0671 time to fit residues: 12.9189 Evaluate side-chains 107 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 827 HIS Chi-restraints excluded: chain A residue 828 PHE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 532 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 97 optimal weight: 0.0370 chunk 87 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 20.0000 chunk 109 optimal weight: 1.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 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 = 0.4530 r_free = 0.4530 target = 0.127881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.100958 restraints weight = 51875.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.103782 restraints weight = 28564.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.105716 restraints weight = 19728.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.106899 restraints weight = 15560.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.107438 restraints weight = 13406.097| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6213 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11633 Z= 0.108 Angle : 0.567 10.686 15773 Z= 0.285 Chirality : 0.040 0.179 1784 Planarity : 0.004 0.055 1984 Dihedral : 8.355 69.748 1653 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.09 % Allowed : 19.73 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.93 (0.23), residues: 1399 helix: 1.16 (0.20), residues: 694 sheet: -0.56 (0.46), residues: 123 loop : 0.40 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 210 TYR 0.018 0.001 TYR A 252 PHE 0.018 0.001 PHE B 266 TRP 0.011 0.001 TRP A 177 HIS 0.003 0.001 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (11633) covalent geometry : angle 0.56658 / 0.29 (15773) hydrogen bonds : bond 0.03737 / 2.54 ( 552) hydrogen bonds : angle 4.67770 / 3.27 ( 1596) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 MET cc_start: 0.8028 (tmm) cc_final: 0.7615 (tmm) REVERT: A 698 THR cc_start: 0.7845 (p) cc_final: 0.7462 (t) REVERT: A 743 MET cc_start: 0.7258 (mmt) cc_final: 0.6906 (mmt) REVERT: A 827 HIS cc_start: 0.7182 (OUTLIER) cc_final: 0.6207 (t-90) REVERT: A 828 PHE cc_start: 0.6703 (OUTLIER) cc_final: 0.6360 (t80) REVERT: A 849 LEU cc_start: 0.8614 (pt) cc_final: 0.8017 (mt) REVERT: B 98 MET cc_start: 0.8023 (ttt) cc_final: 0.7476 (tpp) REVERT: B 101 ASN cc_start: 0.8780 (m110) cc_final: 0.8483 (m110) REVERT: B 270 MET cc_start: 0.5765 (ptp) cc_final: 0.5514 (ptp) REVERT: B 274 MET cc_start: 0.7913 (tmm) cc_final: 0.7074 (mmm) outliers start: 26 outliers final: 17 residues processed: 110 average time/residue: 0.0673 time to fit residues: 12.1593 Evaluate side-chains 105 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 827 HIS Chi-restraints excluded: chain A residue 828 PHE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 532 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 9 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN A 601 GLN A 766 GLN B 377 HIS B 387 HIS B 469 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.126512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.099543 restraints weight = 52216.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.102181 restraints weight = 28780.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.104123 restraints weight = 20016.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.105316 restraints weight = 15828.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.105993 restraints weight = 13638.499| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11633 Z= 0.118 Angle : 0.569 10.134 15773 Z= 0.285 Chirality : 0.041 0.192 1784 Planarity : 0.004 0.058 1984 Dihedral : 8.271 69.296 1653 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.33 % Allowed : 20.21 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.98 (0.23), residues: 1399 helix: 1.27 (0.20), residues: 692 sheet: -0.51 (0.47), residues: 125 loop : 0.34 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 793 TYR 0.018 0.001 TYR A 252 PHE 0.017 0.002 PHE B 96 TRP 0.032 0.002 TRP B 95 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (11633) covalent geometry : angle 0.56858 / 0.29 (15773) hydrogen bonds : bond 0.03716 / 2.51 ( 552) hydrogen bonds : angle 4.61278 / 3.23 ( 1596) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 MET cc_start: 0.8101 (tmm) cc_final: 0.7440 (tmm) REVERT: A 413 GLN cc_start: 0.6913 (mp10) cc_final: 0.6092 (pm20) REVERT: A 698 THR cc_start: 0.7870 (p) cc_final: 0.7476 (t) REVERT: A 743 MET cc_start: 0.7216 (mmt) cc_final: 0.6814 (mmt) REVERT: A 827 HIS cc_start: 0.7174 (OUTLIER) cc_final: 0.6243 (t-90) REVERT: A 849 LEU cc_start: 0.8675 (pt) cc_final: 0.8061 (mt) REVERT: B 98 MET cc_start: 0.8086 (ttt) cc_final: 0.7538 (tpp) REVERT: B 101 ASN cc_start: 0.8837 (m110) cc_final: 0.8570 (m110) REVERT: B 270 MET cc_start: 0.5741 (ptp) cc_final: 0.5276 (ptp) REVERT: B 274 MET cc_start: 0.8027 (tmm) cc_final: 0.7160 (mmm) REVERT: B 418 TYR cc_start: 0.5926 (m-80) cc_final: 0.5534 (m-80) REVERT: B 443 MET cc_start: 0.7585 (ppp) cc_final: 0.7354 (ppp) outliers start: 29 outliers final: 26 residues processed: 110 average time/residue: 0.0746 time to fit residues: 13.2640 Evaluate side-chains 115 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 827 HIS Chi-restraints excluded: chain A residue 828 PHE Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 469 ASN Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain C residue 181 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 4.9990 chunk 79 optimal weight: 0.0670 chunk 29 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 121 optimal weight: 0.0980 overall best weight: 2.4324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 746 ASN ** B 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.123633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.096557 restraints weight = 52973.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.099261 restraints weight = 29642.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.101072 restraints weight = 20653.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.102172 restraints weight = 16460.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.102663 restraints weight = 14291.013| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11633 Z= 0.180 Angle : 0.639 12.522 15773 Z= 0.326 Chirality : 0.043 0.209 1784 Planarity : 0.004 0.066 1984 Dihedral : 8.538 69.552 1653 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.73 % Allowed : 20.53 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.66 (0.23), residues: 1399 helix: 0.98 (0.20), residues: 692 sheet: -0.78 (0.47), residues: 123 loop : 0.25 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 210 TYR 0.018 0.002 TYR A 238 PHE 0.022 0.002 PHE B 467 TRP 0.030 0.003 TRP B 95 HIS 0.024 0.002 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (11633) covalent geometry : angle 0.63938 / 0.33 (15773) hydrogen bonds : bond 0.04251 / 2.87 ( 552) hydrogen bonds : angle 4.86418 / 3.41 ( 1596) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 MET cc_start: 0.8208 (tmm) cc_final: 0.7725 (tmm) REVERT: A 553 THR cc_start: 0.7292 (OUTLIER) cc_final: 0.7071 (p) REVERT: A 698 THR cc_start: 0.7820 (p) cc_final: 0.7432 (t) REVERT: A 827 HIS cc_start: 0.7387 (OUTLIER) cc_final: 0.6346 (t-90) REVERT: A 849 LEU cc_start: 0.8829 (pt) cc_final: 0.8217 (mt) REVERT: B 270 MET cc_start: 0.5815 (ptp) cc_final: 0.5432 (ptp) REVERT: B 274 MET cc_start: 0.8028 (tmm) cc_final: 0.7169 (mmm) REVERT: B 443 MET cc_start: 0.7686 (ppp) cc_final: 0.7332 (ppp) outliers start: 34 outliers final: 30 residues processed: 117 average time/residue: 0.0708 time to fit residues: 13.2335 Evaluate side-chains 116 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 827 HIS Chi-restraints excluded: chain A residue 828 PHE Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 469 ASN Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain C residue 197 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 84 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.123775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.098377 restraints weight = 51897.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.099737 restraints weight = 29230.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.101895 restraints weight = 20852.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.101812 restraints weight = 18235.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.101914 restraints weight = 15543.384| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11633 Z= 0.148 Angle : 0.613 11.162 15773 Z= 0.310 Chirality : 0.042 0.216 1784 Planarity : 0.004 0.061 1984 Dihedral : 8.495 69.486 1653 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.73 % Allowed : 20.85 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.69 (0.23), residues: 1399 helix: 1.01 (0.20), residues: 693 sheet: -0.76 (0.47), residues: 123 loop : 0.24 (0.28), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 240 TYR 0.016 0.001 TYR A 238 PHE 0.019 0.002 PHE B 467 TRP 0.029 0.002 TRP B 95 HIS 0.004 0.001 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (11633) covalent geometry : angle 0.61267 / 0.31 (15773) hydrogen bonds : bond 0.03999 / 2.69 ( 552) hydrogen bonds : angle 4.80383 / 3.36 ( 1596) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 88 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 MET cc_start: 0.8139 (tmm) cc_final: 0.7673 (tmm) REVERT: A 698 THR cc_start: 0.7840 (p) cc_final: 0.7383 (t) REVERT: A 743 MET cc_start: 0.7345 (mmt) cc_final: 0.6943 (mmt) REVERT: A 765 PHE cc_start: 0.4609 (OUTLIER) cc_final: 0.3695 (t80) REVERT: A 827 HIS cc_start: 0.7495 (OUTLIER) cc_final: 0.6443 (t-90) REVERT: A 828 PHE cc_start: 0.7137 (OUTLIER) cc_final: 0.6806 (t80) REVERT: A 849 LEU cc_start: 0.8803 (pt) cc_final: 0.8184 (mt) REVERT: B 98 MET cc_start: 0.8364 (ttt) cc_final: 0.7908 (mmp) REVERT: B 270 MET cc_start: 0.5714 (ptp) cc_final: 0.5359 (ptp) REVERT: B 274 MET cc_start: 0.8088 (tmm) cc_final: 0.7332 (mmm) REVERT: B 443 MET cc_start: 0.7796 (ppp) cc_final: 0.7466 (ppp) REVERT: B 450 TRP cc_start: 0.8909 (t60) cc_final: 0.8592 (t60) REVERT: B 465 LEU cc_start: 0.9322 (pt) cc_final: 0.8986 (mm) outliers start: 34 outliers final: 28 residues processed: 113 average time/residue: 0.0867 time to fit residues: 15.3700 Evaluate side-chains 115 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 765 PHE Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 827 HIS Chi-restraints excluded: chain A residue 828 PHE Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain C residue 197 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 15 optimal weight: 0.1980 chunk 24 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 128 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 34 optimal weight: 0.0060 chunk 117 optimal weight: 10.0000 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 387 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 = 0.4484 r_free = 0.4484 target = 0.124091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.098150 restraints weight = 51420.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.100261 restraints weight = 32368.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.101078 restraints weight = 19842.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.101437 restraints weight = 18335.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.101592 restraints weight = 16459.921| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11633 Z= 0.121 Angle : 0.598 11.237 15773 Z= 0.297 Chirality : 0.041 0.205 1784 Planarity : 0.004 0.059 1984 Dihedral : 8.368 68.950 1653 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.33 % Allowed : 21.49 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.83 (0.23), residues: 1399 helix: 1.14 (0.20), residues: 694 sheet: -0.61 (0.48), residues: 125 loop : 0.27 (0.28), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 210 TYR 0.014 0.001 TYR A 381 PHE 0.016 0.001 PHE B 44 TRP 0.027 0.002 TRP B 95 HIS 0.003 0.001 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (11633) covalent geometry : angle 0.59849 / 0.30 (15773) hydrogen bonds : bond 0.03733 / 2.52 ( 552) hydrogen bonds : angle 4.68416 / 3.28 ( 1596) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 361 MET cc_start: 0.8176 (tmm) cc_final: 0.7771 (tmm) REVERT: A 698 THR cc_start: 0.7777 (p) cc_final: 0.7309 (t) REVERT: A 743 MET cc_start: 0.7256 (mmt) cc_final: 0.6839 (mmt) REVERT: A 765 PHE cc_start: 0.4547 (OUTLIER) cc_final: 0.3643 (t80) REVERT: A 827 HIS cc_start: 0.7490 (OUTLIER) cc_final: 0.6454 (t-90) REVERT: A 828 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.6790 (t80) REVERT: A 849 LEU cc_start: 0.8790 (pt) cc_final: 0.8144 (mt) REVERT: B 98 MET cc_start: 0.8364 (ttt) cc_final: 0.7911 (mmp) REVERT: B 270 MET cc_start: 0.5823 (ptp) cc_final: 0.5428 (ptp) REVERT: B 274 MET cc_start: 0.8170 (tmm) cc_final: 0.7440 (mmt) REVERT: B 443 MET cc_start: 0.7765 (ppp) cc_final: 0.7479 (ppp) outliers start: 29 outliers final: 24 residues processed: 109 average time/residue: 0.0766 time to fit residues: 13.1712 Evaluate side-chains 114 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 765 PHE Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 827 HIS Chi-restraints excluded: chain A residue 828 PHE Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain C residue 181 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 21 optimal weight: 30.0000 chunk 133 optimal weight: 10.0000 chunk 73 optimal weight: 0.0770 chunk 134 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 120 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.0000 chunk 64 optimal weight: 6.9990 overall best weight: 0.7746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 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 = 0.4514 r_free = 0.4514 target = 0.131885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.103779 restraints weight = 48594.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.106691 restraints weight = 26986.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.108621 restraints weight = 18738.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.109831 restraints weight = 14810.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.110494 restraints weight = 12705.934| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11633 Z= 0.108 Angle : 0.588 11.436 15773 Z= 0.291 Chirality : 0.041 0.208 1784 Planarity : 0.004 0.056 1984 Dihedral : 8.249 68.144 1653 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.92 % Allowed : 21.97 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 1.00 (0.23), residues: 1399 helix: 1.32 (0.20), residues: 690 sheet: -0.52 (0.48), residues: 124 loop : 0.30 (0.28), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 210 TYR 0.013 0.001 TYR A 381 PHE 0.016 0.001 PHE B 44 TRP 0.025 0.002 TRP B 338 HIS 0.003 0.001 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (11633) covalent geometry : angle 0.58817 / 0.29 (15773) hydrogen bonds : bond 0.03539 / 2.40 ( 552) hydrogen bonds : angle 4.52654 / 3.18 ( 1596) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 252 TYR cc_start: 0.8191 (t80) cc_final: 0.7670 (t80) REVERT: A 361 MET cc_start: 0.8153 (tmm) cc_final: 0.7846 (tmm) REVERT: A 608 GLU cc_start: 0.8199 (tp30) cc_final: 0.7433 (tp30) REVERT: A 698 THR cc_start: 0.7663 (p) cc_final: 0.7215 (t) REVERT: A 743 MET cc_start: 0.7260 (mmt) cc_final: 0.6875 (mmt) REVERT: A 765 PHE cc_start: 0.4543 (OUTLIER) cc_final: 0.3614 (t80) REVERT: A 827 HIS cc_start: 0.7306 (OUTLIER) cc_final: 0.6359 (t-90) REVERT: A 828 PHE cc_start: 0.7047 (OUTLIER) cc_final: 0.6703 (t80) REVERT: A 849 LEU cc_start: 0.8730 (pt) cc_final: 0.8094 (mt) REVERT: B 98 MET cc_start: 0.8131 (ttt) cc_final: 0.7854 (mmp) REVERT: B 101 ASN cc_start: 0.8909 (m110) cc_final: 0.8520 (p0) REVERT: B 270 MET cc_start: 0.5725 (ptp) cc_final: 0.5409 (ptp) REVERT: B 274 MET cc_start: 0.8168 (tmm) cc_final: 0.7371 (mmm) REVERT: B 443 MET cc_start: 0.7815 (ppp) cc_final: 0.7442 (ppp) outliers start: 24 outliers final: 19 residues processed: 112 average time/residue: 0.0757 time to fit residues: 13.7387 Evaluate side-chains 114 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 765 PHE Chi-restraints excluded: chain A residue 827 HIS Chi-restraints excluded: chain A residue 828 PHE Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain C residue 197 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 134 optimal weight: 0.0000 chunk 58 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 119 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 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 = 0.4474 r_free = 0.4474 target = 0.121882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.094787 restraints weight = 51616.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.097558 restraints weight = 28042.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.099440 restraints weight = 19034.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.100579 restraints weight = 14895.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.101444 restraints weight = 12783.610| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11633 Z= 0.116 Angle : 0.597 11.308 15773 Z= 0.297 Chirality : 0.041 0.207 1784 Planarity : 0.004 0.057 1984 Dihedral : 8.209 67.501 1653 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.00 % Allowed : 22.05 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.98 (0.23), residues: 1399 helix: 1.30 (0.20), residues: 690 sheet: -0.46 (0.49), residues: 124 loop : 0.26 (0.28), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 210 TYR 0.014 0.001 TYR A 381 PHE 0.015 0.001 PHE B 44 TRP 0.051 0.002 TRP B 431 HIS 0.002 0.001 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (11633) covalent geometry : angle 0.59654 / 0.30 (15773) hydrogen bonds : bond 0.03590 / 2.42 ( 552) hydrogen bonds : angle 4.56927 / 3.22 ( 1596) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2067.82 seconds wall clock time: 36 minutes 32.01 seconds (2192.01 seconds total)