Starting phenix.real_space_refine on Wed Feb 4 16:20:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qdq_53032/02_2026/9qdq_53032.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qdq_53032/02_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_53032/02_2026/9qdq_53032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qdq_53032/02_2026/9qdq_53032.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qdq_53032/02_2026/9qdq_53032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qdq_53032/02_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-2.0-5952/lib/python3.9/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: 2.19, per 1000 atoms: 0.19 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: 0.92 Conformation dependent library (CDL) restraints added in 509.8 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: 0.42 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: 1.89 Time building geometry restraints manager: 1.22 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: 2.960 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.740 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5902 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= 0.145 Angle : 0.752 10.530 15773 Z= 0.380 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 covalent geometry : bond 0.00320 (11633) covalent geometry : angle 0.75218 (15773) hydrogen bonds : bond 0.16970 ( 552) hydrogen bonds : angle 6.59891 ( 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 : 0.518 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: 0.1089 time to fit residues: 17.3744 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 : 0.499 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 422 GLN B 101 ASN ** B 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 448 ASN ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.134199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.106166 restraints weight = 47112.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.109129 restraints weight = 26387.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.111210 restraints weight = 18292.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.112635 restraints weight = 14501.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.113468 restraints weight = 12402.717| |-----------------------------------------------------------------------------| r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5927 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11633 Z= 0.139 Angle : 0.616 8.204 15773 Z= 0.320 Chirality : 0.042 0.183 1784 Planarity : 0.004 0.043 1984 Dihedral : 8.765 73.973 1663 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.09 % Allowed : 19.49 % Favored : 78.43 % 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: -0.04 (0.47), residues: 125 loop : 0.44 (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 0.036 0.002 PHE B 266 TRP 0.019 0.002 TRP B 431 HIS 0.004 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00304 (11633) covalent geometry : angle 0.61588 (15773) hydrogen bonds : bond 0.04397 ( 552) hydrogen bonds : angle 5.18963 ( 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 129 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 ASP cc_start: 0.8036 (t0) cc_final: 0.7811 (t0) REVERT: A 743 MET cc_start: 0.7003 (mmt) cc_final: 0.6508 (mmt) REVERT: A 849 LEU cc_start: 0.8555 (pt) cc_final: 0.8039 (mt) REVERT: B 377 HIS cc_start: 0.7895 (m170) cc_final: 0.7675 (m90) REVERT: B 443 MET cc_start: 0.7521 (ppp) cc_final: 0.7230 (ppp) outliers start: 26 outliers final: 13 residues processed: 122 average time/residue: 0.0881 time to fit residues: 16.9752 Evaluate side-chains 100 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 135 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 121 optimal weight: 5.9990 chunk 26 optimal weight: 0.0870 chunk 113 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 overall best weight: 1.4760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 181 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 ASN B 421 HIS C 201 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.129142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.102064 restraints weight = 52427.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.105107 restraints weight = 28722.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.107059 restraints weight = 19687.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.108297 restraints weight = 15500.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.108987 restraints weight = 13329.054| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11633 Z= 0.144 Angle : 0.602 10.192 15773 Z= 0.307 Chirality : 0.042 0.243 1784 Planarity : 0.004 0.056 1984 Dihedral : 8.318 66.037 1653 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.13 % Allowed : 17.72 % Favored : 79.15 % 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: 0.86 (0.23), residues: 1399 helix: 1.03 (0.20), residues: 691 sheet: -0.48 (0.44), residues: 123 loop : 0.45 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 554 TYR 0.015 0.002 TYR B 148 PHE 0.020 0.002 PHE B 266 TRP 0.022 0.002 TRP B 431 HIS 0.004 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00319 (11633) covalent geometry : angle 0.60242 (15773) hydrogen bonds : bond 0.04314 ( 552) hydrogen bonds : angle 4.94829 ( 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 136 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 97 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 ASP cc_start: 0.8021 (t0) cc_final: 0.7818 (t0) REVERT: A 698 THR cc_start: 0.8042 (OUTLIER) cc_final: 0.7702 (t) REVERT: A 743 MET cc_start: 0.7088 (mmt) cc_final: 0.6583 (mmt) REVERT: A 827 HIS cc_start: 0.7145 (OUTLIER) cc_final: 0.6073 (t-90) REVERT: A 849 LEU cc_start: 0.8587 (pt) cc_final: 0.8076 (mt) REVERT: B 274 MET cc_start: 0.7757 (tmm) cc_final: 0.6946 (mmm) REVERT: B 443 MET cc_start: 0.7530 (ppp) cc_final: 0.7300 (ppp) outliers start: 39 outliers final: 14 residues processed: 124 average time/residue: 0.0910 time to fit residues: 17.6343 Evaluate side-chains 102 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 698 THR 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: 0.1980 chunk 26 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 120 optimal weight: 30.0000 chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.127096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.100210 restraints weight = 52471.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.102911 restraints weight = 28621.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.104837 restraints weight = 19827.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.106021 restraints weight = 15624.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.106551 restraints weight = 13472.903| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11633 Z= 0.161 Angle : 0.621 11.195 15773 Z= 0.318 Chirality : 0.042 0.178 1784 Planarity : 0.004 0.062 1984 Dihedral : 8.431 67.700 1653 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.65 % Allowed : 19.25 % Favored : 78.11 % 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: 0.79 (0.23), residues: 1399 helix: 1.01 (0.20), residues: 693 sheet: -0.56 (0.45), residues: 120 loop : 0.37 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 639 TYR 0.017 0.002 TYR A 252 PHE 0.021 0.002 PHE B 15 TRP 0.013 0.002 TRP A 353 HIS 0.005 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00357 (11633) covalent geometry : angle 0.62063 (15773) hydrogen bonds : bond 0.04075 ( 552) hydrogen bonds : angle 4.91531 ( 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 124 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 ASP cc_start: 0.8121 (t0) cc_final: 0.7888 (t0) REVERT: A 743 MET cc_start: 0.7268 (mmt) cc_final: 0.6714 (mmt) REVERT: A 827 HIS cc_start: 0.7242 (OUTLIER) cc_final: 0.6171 (t-90) REVERT: A 849 LEU cc_start: 0.8691 (pt) cc_final: 0.8111 (mt) REVERT: B 270 MET cc_start: 0.5912 (ptp) cc_final: 0.5661 (ptp) REVERT: B 274 MET cc_start: 0.7953 (tmm) cc_final: 0.7027 (mmm) REVERT: B 443 MET cc_start: 0.7589 (ppp) cc_final: 0.7195 (ppp) outliers start: 33 outliers final: 20 residues processed: 115 average time/residue: 0.0814 time to fit residues: 15.1939 Evaluate side-chains 104 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 157 ASN Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 204 LYS 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 575 THR Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 757 VAL 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 505 MET 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: 9.9990 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** 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 101 ASN ** B 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.128119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.101523 restraints weight = 51783.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.104373 restraints weight = 32933.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.105721 restraints weight = 19397.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.105896 restraints weight = 18773.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.106058 restraints weight = 15865.290| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11633 Z= 0.111 Angle : 0.567 13.067 15773 Z= 0.284 Chirality : 0.040 0.177 1784 Planarity : 0.004 0.057 1984 Dihedral : 8.297 69.253 1653 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.04 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: 0.99 (0.23), residues: 1399 helix: 1.24 (0.20), residues: 693 sheet: -0.57 (0.45), residues: 123 loop : 0.40 (0.28), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 210 TYR 0.015 0.001 TYR A 252 PHE 0.024 0.001 PHE B 15 TRP 0.010 0.001 TRP B 338 HIS 0.003 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00241 (11633) covalent geometry : angle 0.56652 (15773) hydrogen bonds : bond 0.03687 ( 552) hydrogen bonds : angle 4.66577 ( 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 115 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 ASP cc_start: 0.8164 (t0) cc_final: 0.7860 (t0) REVERT: A 698 THR cc_start: 0.7925 (p) cc_final: 0.7537 (t) REVERT: A 743 MET cc_start: 0.7111 (mmt) cc_final: 0.6635 (mmt) REVERT: A 827 HIS cc_start: 0.7103 (OUTLIER) cc_final: 0.6138 (t-90) REVERT: A 828 PHE cc_start: 0.6760 (OUTLIER) cc_final: 0.6406 (t80) REVERT: A 849 LEU cc_start: 0.8639 (pt) cc_final: 0.8017 (mt) REVERT: B 274 MET cc_start: 0.7963 (tmm) cc_final: 0.7226 (mmp) REVERT: B 443 MET cc_start: 0.7541 (ppp) cc_final: 0.7317 (ppp) outliers start: 26 outliers final: 16 residues processed: 109 average time/residue: 0.0821 time to fit residues: 14.6739 Evaluate side-chains 105 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 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 656 SER 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 532 LEU Chi-restraints excluded: chain B residue 561 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 10 optimal weight: 0.0770 chunk 53 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** A 181 GLN ** 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** B 413 ASN B 469 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.124695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.097631 restraints weight = 52433.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.100346 restraints weight = 28970.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.102162 restraints weight = 20111.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.103219 restraints weight = 15942.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.104032 restraints weight = 13847.644| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11633 Z= 0.159 Angle : 0.637 13.294 15773 Z= 0.320 Chirality : 0.042 0.197 1784 Planarity : 0.004 0.069 1984 Dihedral : 8.470 69.227 1653 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.05 % Allowed : 19.57 % Favored : 77.39 % 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: 0.76 (0.23), residues: 1399 helix: 1.01 (0.20), residues: 694 sheet: -0.76 (0.46), residues: 123 loop : 0.37 (0.28), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 609 TYR 0.020 0.002 TYR A 252 PHE 0.020 0.002 PHE B 15 TRP 0.015 0.002 TRP A 353 HIS 0.004 0.001 HIS A 629 Details of bonding type rmsd covalent geometry : bond 0.00355 (11633) covalent geometry : angle 0.63739 (15773) hydrogen bonds : bond 0.04125 ( 552) hydrogen bonds : angle 4.81749 ( 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 128 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 90 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 ASP cc_start: 0.8144 (t0) cc_final: 0.7846 (t0) REVERT: A 361 MET cc_start: 0.7965 (tmm) cc_final: 0.7500 (tmm) REVERT: A 608 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7142 (mm-30) REVERT: A 609 ARG cc_start: 0.8137 (ttp80) cc_final: 0.7772 (ttm170) REVERT: A 743 MET cc_start: 0.7255 (mmt) cc_final: 0.6768 (mmt) REVERT: A 827 HIS cc_start: 0.7304 (OUTLIER) cc_final: 0.6276 (t-90) REVERT: A 849 LEU cc_start: 0.8808 (pt) cc_final: 0.8212 (mt) REVERT: B 98 MET cc_start: 0.8296 (ttt) cc_final: 0.7890 (mmp) REVERT: B 274 MET cc_start: 0.8012 (tmm) cc_final: 0.7099 (mmm) REVERT: B 418 TYR cc_start: 0.6020 (m-80) cc_final: 0.5613 (m-80) REVERT: B 443 MET cc_start: 0.7658 (ppp) cc_final: 0.7324 (ppp) outliers start: 38 outliers final: 29 residues processed: 119 average time/residue: 0.0920 time to fit residues: 17.0831 Evaluate side-chains 112 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 82 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 249 GLU 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 575 THR Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 757 VAL 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 469 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN ** A 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 GLN B 21 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN B 469 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.125292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.097508 restraints weight = 49074.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.099957 restraints weight = 28723.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.101569 restraints weight = 20587.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.102689 restraints weight = 16715.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.103169 restraints weight = 14563.726| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 11633 Z= 0.257 Angle : 0.773 12.261 15773 Z= 0.401 Chirality : 0.047 0.250 1784 Planarity : 0.005 0.074 1984 Dihedral : 8.936 68.463 1653 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.69 % Allowed : 19.49 % Favored : 76.82 % 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: 0.16 (0.23), residues: 1399 helix: 0.52 (0.19), residues: 695 sheet: -1.06 (0.46), residues: 120 loop : 0.06 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 210 TYR 0.021 0.003 TYR A 238 PHE 0.042 0.003 PHE B 467 TRP 0.024 0.003 TRP A 353 HIS 0.006 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00579 (11633) covalent geometry : angle 0.77341 (15773) hydrogen bonds : bond 0.05050 ( 552) hydrogen bonds : angle 5.26922 ( 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 133 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 87 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 MET cc_start: 0.8251 (tmm) cc_final: 0.7754 (tmm) REVERT: A 608 GLU cc_start: 0.7759 (tm-30) cc_final: 0.6912 (mm-30) REVERT: A 609 ARG cc_start: 0.8264 (ttp80) cc_final: 0.8026 (ttm170) REVERT: A 765 PHE cc_start: 0.4664 (OUTLIER) cc_final: 0.3744 (t80) REVERT: A 827 HIS cc_start: 0.7591 (OUTLIER) cc_final: 0.6535 (t-90) REVERT: A 849 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8311 (mt) REVERT: B 98 MET cc_start: 0.8365 (ttt) cc_final: 0.8103 (mmp) REVERT: B 270 MET cc_start: 0.5824 (ptp) cc_final: 0.5593 (ptp) REVERT: B 274 MET cc_start: 0.8105 (tmm) cc_final: 0.7265 (mmm) REVERT: B 443 MET cc_start: 0.7867 (ppp) cc_final: 0.7475 (ppp) outliers start: 46 outliers final: 33 residues processed: 125 average time/residue: 0.0945 time to fit residues: 18.1431 Evaluate side-chains 114 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 78 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 123 TYR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 145 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 213 ILE Chi-restraints excluded: chain A residue 249 GLU 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 575 THR Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 693 ILE 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 757 VAL Chi-restraints excluded: chain A residue 765 PHE Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 827 HIS Chi-restraints excluded: chain A residue 828 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 548 SER 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: 0.0030 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 121 optimal weight: 0.0770 chunk 86 optimal weight: 0.6980 overall best weight: 0.4948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 181 GLN B 265 ASN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.124411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.097394 restraints weight = 51365.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.100104 restraints weight = 28531.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.101913 restraints weight = 19767.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.103069 restraints weight = 15642.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.103796 restraints weight = 13502.859| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11633 Z= 0.112 Angle : 0.625 10.959 15773 Z= 0.310 Chirality : 0.042 0.261 1784 Planarity : 0.004 0.057 1984 Dihedral : 8.547 70.288 1653 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.68 % Allowed : 21.89 % 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: 0.73 (0.23), residues: 1399 helix: 1.05 (0.20), residues: 689 sheet: -0.74 (0.46), residues: 123 loop : 0.26 (0.28), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 100 TYR 0.017 0.001 TYR A 378 PHE 0.018 0.002 PHE B 15 TRP 0.024 0.002 TRP B 338 HIS 0.002 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00233 (11633) covalent geometry : angle 0.62503 (15773) hydrogen bonds : bond 0.03824 ( 552) hydrogen bonds : angle 4.74667 ( 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 113 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 608 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7142 (mm-30) REVERT: A 698 THR cc_start: 0.7625 (p) cc_final: 0.7173 (t) REVERT: A 743 MET cc_start: 0.7336 (mmt) cc_final: 0.6843 (mmt) REVERT: A 827 HIS cc_start: 0.7505 (OUTLIER) cc_final: 0.6455 (t-90) REVERT: A 828 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.6752 (t80) REVERT: A 849 LEU cc_start: 0.8716 (pt) cc_final: 0.8054 (mt) REVERT: B 98 MET cc_start: 0.8306 (ttt) cc_final: 0.8033 (mmp) REVERT: B 270 MET cc_start: 0.5832 (ptp) cc_final: 0.5584 (ptp) REVERT: B 274 MET cc_start: 0.8103 (tmm) cc_final: 0.7355 (mmm) REVERT: B 443 MET cc_start: 0.7795 (ppp) cc_final: 0.7467 (ppp) outliers start: 21 outliers final: 13 residues processed: 106 average time/residue: 0.0929 time to fit residues: 15.5337 Evaluate side-chains 99 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 204 LYS Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 656 SER 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 387 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 15 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 462 ASN ** A 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.116700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.090798 restraints weight = 53330.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.092580 restraints weight = 33879.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.093471 restraints weight = 22250.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.093652 restraints weight = 21015.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.093704 restraints weight = 18249.012| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.6145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 11633 Z= 0.367 Angle : 0.941 15.802 15773 Z= 0.492 Chirality : 0.053 0.345 1784 Planarity : 0.006 0.085 1984 Dihedral : 9.222 65.572 1653 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.86 % Favored : 94.07 % Rotamer: Outliers : 2.89 % Allowed : 21.09 % Favored : 76.02 % 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: -0.36 (0.22), residues: 1399 helix: 0.14 (0.19), residues: 688 sheet: -1.19 (0.47), residues: 121 loop : -0.29 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG C 210 TYR 0.033 0.004 TYR A 238 PHE 0.030 0.004 PHE A 83 TRP 0.047 0.004 TRP B 338 HIS 0.018 0.003 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00817 (11633) covalent geometry : angle 0.94051 (15773) hydrogen bonds : bond 0.06073 ( 552) hydrogen bonds : angle 5.81356 ( 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 121 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 85 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASN cc_start: 0.1269 (OUTLIER) cc_final: 0.1039 (m-40) REVERT: A 608 GLU cc_start: 0.8117 (tm-30) cc_final: 0.6993 (mm-30) REVERT: A 743 MET cc_start: 0.7438 (mmt) cc_final: 0.6900 (mmt) REVERT: A 765 PHE cc_start: 0.4704 (OUTLIER) cc_final: 0.3642 (t80) REVERT: A 849 LEU cc_start: 0.9146 (pt) cc_final: 0.8389 (mt) REVERT: B 98 MET cc_start: 0.8646 (ttt) cc_final: 0.8313 (mmp) REVERT: B 125 LYS cc_start: 0.8948 (mttt) cc_final: 0.8545 (mttt) REVERT: B 270 MET cc_start: 0.5737 (ptp) cc_final: 0.5189 (ptp) REVERT: B 274 MET cc_start: 0.8249 (tmm) cc_final: 0.7421 (mmp) REVERT: B 443 MET cc_start: 0.8054 (ppp) cc_final: 0.7717 (ppp) outliers start: 36 outliers final: 25 residues processed: 113 average time/residue: 0.0972 time to fit residues: 16.7822 Evaluate side-chains 105 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 693 ILE 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 757 VAL Chi-restraints excluded: chain A residue 765 PHE Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 828 PHE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 558 VAL 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 21 optimal weight: 40.0000 chunk 133 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.120983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.094053 restraints weight = 52646.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.096467 restraints weight = 29249.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.098197 restraints weight = 20483.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.099284 restraints weight = 16364.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.099730 restraints weight = 14199.930| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.6064 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= 0.142 Angle : 0.685 15.593 15773 Z= 0.345 Chirality : 0.043 0.303 1784 Planarity : 0.005 0.068 1984 Dihedral : 8.754 66.911 1653 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.60 % Allowed : 22.94 % Favored : 75.46 % 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: 0.23 (0.23), residues: 1399 helix: 0.75 (0.19), residues: 692 sheet: -1.03 (0.45), residues: 131 loop : -0.13 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 100 TYR 0.021 0.002 TYR A 381 PHE 0.017 0.002 PHE B 15 TRP 0.048 0.003 TRP B 338 HIS 0.006 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00309 (11633) covalent geometry : angle 0.68497 (15773) hydrogen bonds : bond 0.04335 ( 552) hydrogen bonds : angle 5.08146 ( 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 113 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 608 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7154 (mm-30) REVERT: B 98 MET cc_start: 0.8467 (ttt) cc_final: 0.8169 (mmp) REVERT: B 115 LYS cc_start: 0.6897 (mttt) cc_final: 0.6695 (mttt) REVERT: B 270 MET cc_start: 0.5708 (ptp) cc_final: 0.5054 (ptp) REVERT: B 274 MET cc_start: 0.8150 (tmm) cc_final: 0.7432 (mmm) REVERT: B 286 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7638 (pp) REVERT: B 443 MET cc_start: 0.7819 (ppp) cc_final: 0.7510 (ppp) REVERT: C 181 MET cc_start: 0.1388 (OUTLIER) cc_final: 0.1137 (tmm) outliers start: 20 outliers final: 14 residues processed: 109 average time/residue: 0.0977 time to fit residues: 16.3226 Evaluate side-chains 99 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 828 PHE Chi-restraints excluded: chain B residue 286 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: 1.9990 chunk 58 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 chunk 49 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 97 ASN ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.125651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.097836 restraints weight = 50076.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.101105 restraints weight = 31716.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.101369 restraints weight = 18190.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.101879 restraints weight = 18772.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.101980 restraints weight = 16483.211| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11633 Z= 0.125 Angle : 0.668 15.679 15773 Z= 0.329 Chirality : 0.043 0.290 1784 Planarity : 0.004 0.059 1984 Dihedral : 8.450 65.588 1653 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.44 % Allowed : 23.34 % Favored : 75.22 % 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: 0.53 (0.23), residues: 1399 helix: 1.00 (0.20), residues: 693 sheet: -0.90 (0.45), residues: 131 loop : 0.03 (0.28), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 100 TYR 0.017 0.001 TYR A 381 PHE 0.017 0.001 PHE B 376 TRP 0.035 0.002 TRP B 338 HIS 0.002 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00275 (11633) covalent geometry : angle 0.66845 (15773) hydrogen bonds : bond 0.03934 ( 552) hydrogen bonds : angle 4.82821 ( 1596) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2424.61 seconds wall clock time: 42 minutes 53.67 seconds (2573.67 seconds total)