Starting phenix.real_space_refine on Wed May 14 01:41:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jqi_36573/05_2025/8jqi_36573_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jqi_36573/05_2025/8jqi_36573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jqi_36573/05_2025/8jqi_36573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jqi_36573/05_2025/8jqi_36573.map" model { file = "/net/cci-nas-00/data/ceres_data/8jqi_36573/05_2025/8jqi_36573_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jqi_36573/05_2025/8jqi_36573_neut.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.064 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 7121 2.51 5 N 1917 2.21 5 O 2079 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11180 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8716 Classifications: {'peptide': 1062} Link IDs: {'PTRANS': 47, 'TRANS': 1014} Chain breaks: 4 Chain: "B" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2464 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 18, 'TRANS': 288} Time building chain proxies: 6.53, per 1000 atoms: 0.58 Number of scatterers: 11180 At special positions: 0 Unit cell: (108.9, 102.3, 152.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 2079 8.00 N 1917 7.00 C 7121 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: 2.97 Conformation dependent library (CDL) restraints added in 1.5 seconds 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2614 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 17 sheets defined 35.2% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 11 through 25 removed outlier: 3.776A pdb=" N GLN A 17 " --> pdb=" O TYR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 136 Processing helix chain 'A' and resid 137 through 154 removed outlier: 3.909A pdb=" N ASP A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 173 Proline residue: A 171 - end of helix Processing helix chain 'A' and resid 180 through 191 removed outlier: 4.167A pdb=" N LYS A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 223 removed outlier: 5.839A pdb=" N SER A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE A 217 " --> pdb=" O GLN A 213 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS A 223 " --> pdb=" O ASP A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 253 Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 261 through 274 removed outlier: 3.663A pdb=" N VAL A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 297 through 300 Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.713A pdb=" N TYR A 306 " --> pdb=" O ASP A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 315 removed outlier: 3.662A pdb=" N ASN A 315 " --> pdb=" O GLN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 341 through 352 removed outlier: 3.956A pdb=" N TYR A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 352 " --> pdb=" O CYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 392 Processing helix chain 'A' and resid 410 through 426 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 539 through 554 removed outlier: 3.666A pdb=" N THR A 554 " --> pdb=" O TYR A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 620 removed outlier: 4.001A pdb=" N LEU A 613 " --> pdb=" O SER A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 644 Processing helix chain 'A' and resid 652 through 663 Processing helix chain 'A' and resid 712 through 722 removed outlier: 3.901A pdb=" N LYS A 722 " --> pdb=" O SER A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 746 removed outlier: 4.152A pdb=" N ARG A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 843 Processing helix chain 'A' and resid 845 through 849 Processing helix chain 'A' and resid 856 through 858 No H-bonds generated for 'chain 'A' and resid 856 through 858' Processing helix chain 'A' and resid 892 through 908 Processing helix chain 'A' and resid 927 through 934 Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 970 through 979 Processing helix chain 'A' and resid 999 through 1005 Processing helix chain 'A' and resid 1018 through 1034 removed outlier: 4.203A pdb=" N LEU A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ASN A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY A1032 " --> pdb=" O PHE A1028 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR A1034 " --> pdb=" O LEU A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1045 Processing helix chain 'A' and resid 1156 through 1158 No H-bonds generated for 'chain 'A' and resid 1156 through 1158' Processing helix chain 'B' and resid 521 through 539 Processing helix chain 'B' and resid 568 through 575 Processing helix chain 'B' and resid 596 through 617 Processing helix chain 'B' and resid 668 through 674 Processing helix chain 'B' and resid 678 through 695 Processing helix chain 'B' and resid 705 through 715 removed outlier: 3.871A pdb=" N PHE B 710 " --> pdb=" O VAL B 706 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS B 711 " --> pdb=" O GLU B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 737 Processing helix chain 'B' and resid 746 through 762 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 55 removed outlier: 6.474A pdb=" N THR A 37 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER A 32 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A 110 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR A 97 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ILE A 73 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU A 99 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AA3, first strand: chain 'A' and resid 240 through 241 Processing sheet with id=AA4, first strand: chain 'A' and resid 938 through 939 removed outlier: 5.813A pdb=" N LYS A 938 " --> pdb=" O ILE A 955 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N SER A 957 " --> pdb=" O LYS A 938 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU A 954 " --> pdb=" O LEU A 982 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ARG A 984 " --> pdb=" O GLU A 954 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ARG A 956 " --> pdb=" O ARG A 984 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TYR A 986 " --> pdb=" O ARG A 956 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE A 958 " --> pdb=" O TYR A 986 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR A 983 " --> pdb=" O MET A1009 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ALA A1011 " --> pdb=" O THR A 983 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL A 985 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL A1010 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE A 323 " --> pdb=" O VAL A1010 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N LEU A1012 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N SER A 325 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 355 through 358 removed outlier: 6.400A pdb=" N ILE A 356 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 401 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LYS A 454 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU A 403 " --> pdb=" O LYS A 454 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 360 through 361 removed outlier: 3.767A pdb=" N VAL A 369 " --> pdb=" O TRP A 361 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 370 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 380 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 478 through 484 removed outlier: 6.970A pdb=" N ARG A 493 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASP A 508 " --> pdb=" O ARG A 493 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N TYR A 495 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 563 through 565 Processing sheet with id=AA9, first strand: chain 'A' and resid 577 through 579 Processing sheet with id=AB1, first strand: chain 'A' and resid 590 through 593 removed outlier: 3.620A pdb=" N LEU A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 622 through 623 Processing sheet with id=AB3, first strand: chain 'A' and resid 647 through 648 removed outlier: 3.925A pdb=" N LYS A 673 " --> pdb=" O TYR A 648 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA A 668 " --> pdb=" O ARG A 685 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 685 " --> pdb=" O ALA A 668 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 647 through 648 removed outlier: 3.925A pdb=" N LYS A 673 " --> pdb=" O TYR A 648 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1124 removed outlier: 5.214A pdb=" N LEU A1063 " --> pdb=" O ARG A1187 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ARG A1187 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL A1065 " --> pdb=" O GLU A1185 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLU A1185 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N VAL A1067 " --> pdb=" O PHE A1183 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N PHE A1183 " --> pdb=" O VAL A1067 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A1069 " --> pdb=" O LEU A1181 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ALA A1178 " --> pdb=" O LEU A1167 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1098 through 1100 removed outlier: 3.518A pdb=" N ALA A1149 " --> pdb=" O VAL A1136 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU A1138 " --> pdb=" O PHE A1147 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N PHE A1147 " --> pdb=" O GLU A1138 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 478 through 486 removed outlier: 5.453A pdb=" N LEU B 494 " --> pdb=" O GLY B 481 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL B 492 " --> pdb=" O PRO B 483 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N GLY B 485 " --> pdb=" O GLY B 490 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLY B 490 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TYR B 558 " --> pdb=" O ALA B 550 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA B 550 " --> pdb=" O TYR B 558 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE B 560 " --> pdb=" O LEU B 548 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 629 through 631 426 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.87 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2434 1.33 - 1.45: 2538 1.45 - 1.57: 6365 1.57 - 1.69: 0 1.69 - 1.81: 101 Bond restraints: 11438 Sorted by residual: bond pdb=" CA LYS A 598 " pdb=" C LYS A 598 " ideal model delta sigma weight residual 1.526 1.474 0.052 1.42e-02 4.96e+03 1.35e+01 bond pdb=" C TYR A1036 " pdb=" N VAL A1037 " ideal model delta sigma weight residual 1.332 1.293 0.039 1.23e-02 6.61e+03 1.01e+01 bond pdb=" CA TYR A1036 " pdb=" C TYR A1036 " ideal model delta sigma weight residual 1.522 1.486 0.036 1.19e-02 7.06e+03 9.16e+00 bond pdb=" C TYR A 600 " pdb=" N LEU A 601 " ideal model delta sigma weight residual 1.335 1.373 -0.038 1.35e-02 5.49e+03 7.74e+00 bond pdb=" CA TYR A1036 " pdb=" CB TYR A1036 " ideal model delta sigma weight residual 1.532 1.489 0.042 1.74e-02 3.30e+03 5.88e+00 ... (remaining 11433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 14814 1.94 - 3.89: 550 3.89 - 5.83: 63 5.83 - 7.78: 16 7.78 - 9.72: 3 Bond angle restraints: 15446 Sorted by residual: angle pdb=" N ILE B 648 " pdb=" CA ILE B 648 " pdb=" C ILE B 648 " ideal model delta sigma weight residual 111.91 106.64 5.27 8.90e-01 1.26e+00 3.50e+01 angle pdb=" C LYS A 223 " pdb=" CA LYS A 223 " pdb=" CB LYS A 223 " ideal model delta sigma weight residual 116.54 110.05 6.49 1.15e+00 7.56e-01 3.18e+01 angle pdb=" N ASP A 633 " pdb=" CA ASP A 633 " pdb=" C ASP A 633 " ideal model delta sigma weight residual 108.47 118.19 -9.72 1.79e+00 3.12e-01 2.95e+01 angle pdb=" N ILE A 229 " pdb=" CA ILE A 229 " pdb=" C ILE A 229 " ideal model delta sigma weight residual 111.56 107.91 3.65 8.60e-01 1.35e+00 1.80e+01 angle pdb=" N ASN A 604 " pdb=" CA ASN A 604 " pdb=" C ASN A 604 " ideal model delta sigma weight residual 111.36 106.75 4.61 1.09e+00 8.42e-01 1.79e+01 ... (remaining 15441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6307 17.99 - 35.98: 549 35.98 - 53.97: 81 53.97 - 71.96: 13 71.96 - 89.96: 11 Dihedral angle restraints: 6961 sinusoidal: 2928 harmonic: 4033 Sorted by residual: dihedral pdb=" CA PHE B 694 " pdb=" C PHE B 694 " pdb=" N THR B 695 " pdb=" CA THR B 695 " ideal model delta harmonic sigma weight residual 180.00 154.61 25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA PHE A 577 " pdb=" C PHE A 577 " pdb=" N TRP A 578 " pdb=" CA TRP A 578 " ideal model delta harmonic sigma weight residual 180.00 160.15 19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA TYR A 321 " pdb=" C TYR A 321 " pdb=" N TRP A 322 " pdb=" CA TRP A 322 " ideal model delta harmonic sigma weight residual 180.00 160.80 19.20 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 6958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1237 0.051 - 0.102: 342 0.102 - 0.154: 80 0.154 - 0.205: 2 0.205 - 0.256: 2 Chirality restraints: 1663 Sorted by residual: chirality pdb=" CB ILE A 453 " pdb=" CA ILE A 453 " pdb=" CG1 ILE A 453 " pdb=" CG2 ILE A 453 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB ILE A 487 " pdb=" CA ILE A 487 " pdb=" CG1 ILE A 487 " pdb=" CG2 ILE A 487 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CG LEU B 767 " pdb=" CB LEU B 767 " pdb=" CD1 LEU B 767 " pdb=" CD2 LEU B 767 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.20 2.00e-01 2.50e+01 9.53e-01 ... (remaining 1660 not shown) Planarity restraints: 1987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1003 " 0.025 2.00e-02 2.50e+03 2.39e-02 1.43e+01 pdb=" CG TRP A1003 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A1003 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP A1003 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1003 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A1003 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1003 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1003 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1003 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A1003 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 577 " 0.271 9.50e-02 1.11e+02 1.21e-01 9.10e+00 pdb=" NE ARG B 577 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 577 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B 577 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 577 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 597 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C LEU A 597 " 0.042 2.00e-02 2.50e+03 pdb=" O LEU A 597 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS A 598 " -0.014 2.00e-02 2.50e+03 ... (remaining 1984 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2102 2.76 - 3.30: 12078 3.30 - 3.83: 19524 3.83 - 4.37: 23240 4.37 - 4.90: 36678 Nonbonded interactions: 93622 Sorted by model distance: nonbonded pdb=" NH2 ARG A 589 " pdb=" OD2 ASP B 755 " model vdw 2.226 3.120 nonbonded pdb=" ND2 ASN A 978 " pdb=" O GLY A1006 " model vdw 2.229 3.120 nonbonded pdb=" OE1 GLU A 407 " pdb=" NE2 HIS A 455 " model vdw 2.237 3.120 nonbonded pdb=" O THR B 678 " pdb=" OG SER B 681 " model vdw 2.241 3.040 nonbonded pdb=" OD1 ASP A 362 " pdb=" NE2 GLN A 413 " model vdw 2.246 3.120 ... (remaining 93617 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=0.01 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.330 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 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 : 0.005 0.057 11438 Z= 0.269 Angle : 0.846 9.719 15446 Z= 0.490 Chirality : 0.048 0.256 1663 Planarity : 0.006 0.121 1987 Dihedral : 13.610 89.955 4347 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 25.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.08 % Allowed : 1.13 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.22), residues: 1357 helix: 0.13 (0.24), residues: 438 sheet: -1.22 (0.37), residues: 209 loop : -0.97 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP A1003 HIS 0.009 0.002 HIS A 494 PHE 0.024 0.003 PHE A1000 TYR 0.031 0.002 TYR A 100 ARG 0.008 0.001 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.12822 ( 425) hydrogen bonds : angle 7.45281 ( 1191) covalent geometry : bond 0.00538 (11438) covalent geometry : angle 0.84648 (15446) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.9061 (pp20) cc_final: 0.8610 (pp20) REVERT: A 171 PRO cc_start: 0.8022 (Cg_exo) cc_final: 0.7645 (Cg_endo) REVERT: A 331 LEU cc_start: 0.8788 (mt) cc_final: 0.8535 (mt) REVERT: A 483 MET cc_start: 0.8122 (mmm) cc_final: 0.7741 (mmt) REVERT: A 845 LEU cc_start: 0.8817 (tp) cc_final: 0.8409 (tp) REVERT: A 946 ASN cc_start: 0.8403 (t0) cc_final: 0.8179 (t0) REVERT: B 515 MET cc_start: 0.4842 (ptt) cc_final: 0.4606 (pmm) REVERT: B 583 TYR cc_start: 0.5286 (m-80) cc_final: 0.5004 (p90) REVERT: B 717 HIS cc_start: 0.8252 (m-70) cc_final: 0.7848 (m-70) outliers start: 1 outliers final: 1 residues processed: 176 average time/residue: 0.2506 time to fit residues: 62.1197 Evaluate side-chains 119 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 106 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN A 214 GLN A 408 HIS ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 HIS A 637 ASN ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 594 GLN B 749 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.117810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.091882 restraints weight = 42190.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.094081 restraints weight = 23554.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.095605 restraints weight = 15227.084| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11438 Z= 0.252 Angle : 0.711 6.768 15446 Z= 0.378 Chirality : 0.046 0.178 1663 Planarity : 0.005 0.051 1987 Dihedral : 5.381 23.130 1504 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.22), residues: 1357 helix: 0.26 (0.23), residues: 457 sheet: -1.52 (0.35), residues: 203 loop : -1.16 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A1003 HIS 0.010 0.002 HIS A 408 PHE 0.023 0.003 PHE A 421 TYR 0.027 0.002 TYR A 600 ARG 0.009 0.001 ARG B 577 Details of bonding type rmsd hydrogen bonds : bond 0.04467 ( 425) hydrogen bonds : angle 6.35733 ( 1191) covalent geometry : bond 0.00553 (11438) covalent geometry : angle 0.71084 (15446) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.7552 (tp30) cc_final: 0.7344 (tp30) REVERT: A 331 LEU cc_start: 0.9300 (mt) cc_final: 0.8803 (mp) REVERT: A 351 MET cc_start: 0.9054 (mtp) cc_final: 0.8355 (mtp) REVERT: A 495 TYR cc_start: 0.7704 (t80) cc_final: 0.7186 (t80) REVERT: A 729 MET cc_start: 0.7883 (ppp) cc_final: 0.7631 (ppp) REVERT: A 845 LEU cc_start: 0.8691 (tp) cc_final: 0.8312 (tp) REVERT: A 1003 TRP cc_start: 0.8736 (m-90) cc_final: 0.8409 (m-90) REVERT: A 1021 MET cc_start: 0.8296 (tpp) cc_final: 0.7855 (tpp) REVERT: B 515 MET cc_start: 0.5849 (ptt) cc_final: 0.5609 (pmm) REVERT: B 717 HIS cc_start: 0.8076 (m-70) cc_final: 0.7759 (m-70) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2434 time to fit residues: 53.1306 Evaluate side-chains 110 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 112 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 88 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 ASN ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 HIS ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.121393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.095473 restraints weight = 46923.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.097267 restraints weight = 27119.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.098517 restraints weight = 17971.643| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11438 Z= 0.174 Angle : 0.618 6.583 15446 Z= 0.329 Chirality : 0.045 0.171 1663 Planarity : 0.004 0.050 1987 Dihedral : 5.133 21.905 1504 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.08 % Allowed : 4.28 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.22), residues: 1357 helix: 0.56 (0.24), residues: 457 sheet: -1.52 (0.35), residues: 205 loop : -1.09 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1003 HIS 0.005 0.001 HIS A 701 PHE 0.031 0.002 PHE A1028 TYR 0.017 0.002 TYR A 151 ARG 0.006 0.000 ARG A 953 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 425) hydrogen bonds : angle 5.97784 ( 1191) covalent geometry : bond 0.00387 (11438) covalent geometry : angle 0.61815 (15446) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7903 (mtm) REVERT: A 313 ASP cc_start: 0.8081 (m-30) cc_final: 0.7870 (m-30) REVERT: A 331 LEU cc_start: 0.9339 (mt) cc_final: 0.8773 (mt) REVERT: A 351 MET cc_start: 0.8885 (mtp) cc_final: 0.8353 (mtp) REVERT: A 415 ARG cc_start: 0.7621 (mtt-85) cc_final: 0.6659 (mtm110) REVERT: A 483 MET cc_start: 0.8318 (mmm) cc_final: 0.8077 (mmt) REVERT: A 495 TYR cc_start: 0.7760 (t80) cc_final: 0.7138 (t80) REVERT: A 729 MET cc_start: 0.7757 (ppp) cc_final: 0.7550 (ppp) REVERT: A 845 LEU cc_start: 0.8762 (tp) cc_final: 0.8364 (tp) REVERT: A 1003 TRP cc_start: 0.8851 (m-90) cc_final: 0.8410 (m-90) REVERT: A 1021 MET cc_start: 0.8475 (tpp) cc_final: 0.8107 (tpp) REVERT: A 1072 HIS cc_start: 0.7356 (m90) cc_final: 0.7116 (m170) REVERT: B 515 MET cc_start: 0.5642 (ptt) cc_final: 0.5345 (pmm) REVERT: B 532 MET cc_start: -0.3717 (mtm) cc_final: -0.3953 (ptp) REVERT: B 701 TYR cc_start: 0.5297 (m-80) cc_final: 0.4786 (m-80) REVERT: B 717 HIS cc_start: 0.8218 (m-70) cc_final: 0.7933 (m-70) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.2344 time to fit residues: 51.5850 Evaluate side-chains 116 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 121 optimal weight: 0.3980 chunk 112 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 HIS A 744 ASN ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.121355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.095454 restraints weight = 40708.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.097878 restraints weight = 22607.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.099470 restraints weight = 14420.690| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3825 r_free = 0.3825 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3824 r_free = 0.3824 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11438 Z= 0.120 Angle : 0.581 9.293 15446 Z= 0.303 Chirality : 0.044 0.204 1663 Planarity : 0.004 0.048 1987 Dihedral : 4.808 19.613 1504 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.22), residues: 1357 helix: 0.79 (0.24), residues: 459 sheet: -1.41 (0.36), residues: 194 loop : -0.98 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 578 HIS 0.005 0.001 HIS A1025 PHE 0.013 0.002 PHE A1000 TYR 0.029 0.001 TYR A 206 ARG 0.006 0.000 ARG A 700 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 425) hydrogen bonds : angle 5.63229 ( 1191) covalent geometry : bond 0.00265 (11438) covalent geometry : angle 0.58118 (15446) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8191 (mmm) cc_final: 0.7948 (mmm) REVERT: A 173 ILE cc_start: 0.8265 (pt) cc_final: 0.8056 (pt) REVERT: A 313 ASP cc_start: 0.8018 (m-30) cc_final: 0.7783 (m-30) REVERT: A 331 LEU cc_start: 0.9238 (mt) cc_final: 0.8786 (mt) REVERT: A 351 MET cc_start: 0.8909 (mtp) cc_final: 0.8291 (mtp) REVERT: A 495 TYR cc_start: 0.7868 (t80) cc_final: 0.7231 (t80) REVERT: A 845 LEU cc_start: 0.8730 (tp) cc_final: 0.8300 (tp) REVERT: A 1003 TRP cc_start: 0.8823 (m-10) cc_final: 0.8460 (m-90) REVERT: B 717 HIS cc_start: 0.8113 (m-70) cc_final: 0.7781 (m-70) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2387 time to fit residues: 53.9553 Evaluate side-chains 116 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 84 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.117508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.092272 restraints weight = 42110.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.094468 restraints weight = 23922.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.095890 restraints weight = 15625.459| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11438 Z= 0.225 Angle : 0.660 7.137 15446 Z= 0.350 Chirality : 0.045 0.174 1663 Planarity : 0.005 0.051 1987 Dihedral : 5.100 20.506 1504 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.22), residues: 1357 helix: 0.55 (0.24), residues: 456 sheet: -1.59 (0.35), residues: 199 loop : -1.11 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1003 HIS 0.006 0.002 HIS A1025 PHE 0.023 0.002 PHE A 952 TYR 0.028 0.002 TYR A 206 ARG 0.005 0.001 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 425) hydrogen bonds : angle 5.96232 ( 1191) covalent geometry : bond 0.00490 (11438) covalent geometry : angle 0.65977 (15446) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8165 (mmm) cc_final: 0.7938 (mmm) REVERT: A 313 ASP cc_start: 0.8037 (m-30) cc_final: 0.7824 (m-30) REVERT: A 331 LEU cc_start: 0.9340 (mt) cc_final: 0.8897 (mt) REVERT: A 376 ARG cc_start: 0.7258 (mmp-170) cc_final: 0.6888 (mmm160) REVERT: A 495 TYR cc_start: 0.8010 (t80) cc_final: 0.7286 (t80) REVERT: A 845 LEU cc_start: 0.8720 (tp) cc_final: 0.8200 (tp) REVERT: A 1003 TRP cc_start: 0.8978 (m-10) cc_final: 0.8416 (m-90) REVERT: A 1021 MET cc_start: 0.8580 (tpp) cc_final: 0.8144 (tpp) REVERT: B 675 ARG cc_start: 0.8082 (mtt180) cc_final: 0.7399 (mmt-90) REVERT: B 717 HIS cc_start: 0.7891 (m-70) cc_final: 0.7600 (m-70) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2587 time to fit residues: 56.3549 Evaluate side-chains 114 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 90 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS A 214 GLN ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 HIS A 990 GLN ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 749 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.118455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.092010 restraints weight = 44024.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.094231 restraints weight = 24864.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.095685 restraints weight = 16204.909| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11438 Z= 0.160 Angle : 0.607 6.830 15446 Z= 0.321 Chirality : 0.045 0.301 1663 Planarity : 0.004 0.049 1987 Dihedral : 4.980 19.962 1504 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.22), residues: 1357 helix: 0.57 (0.24), residues: 457 sheet: -1.61 (0.35), residues: 204 loop : -1.09 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 578 HIS 0.007 0.001 HIS A 203 PHE 0.021 0.002 PHE A 952 TYR 0.029 0.002 TYR A 206 ARG 0.004 0.000 ARG A 618 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 425) hydrogen bonds : angle 5.74501 ( 1191) covalent geometry : bond 0.00351 (11438) covalent geometry : angle 0.60744 (15446) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8167 (mmm) cc_final: 0.7870 (mmm) REVERT: A 313 ASP cc_start: 0.8068 (m-30) cc_final: 0.7830 (m-30) REVERT: A 331 LEU cc_start: 0.9314 (mt) cc_final: 0.8891 (mt) REVERT: A 376 ARG cc_start: 0.7216 (mmp-170) cc_final: 0.6822 (mmm160) REVERT: A 495 TYR cc_start: 0.7967 (t80) cc_final: 0.7312 (t80) REVERT: A 592 MET cc_start: 0.1568 (ptp) cc_final: 0.1216 (ptp) REVERT: A 728 LYS cc_start: 0.8539 (tptp) cc_final: 0.8276 (tptp) REVERT: A 845 LEU cc_start: 0.8738 (tp) cc_final: 0.8283 (tp) REVERT: A 1003 TRP cc_start: 0.9009 (m-10) cc_final: 0.8488 (m-90) REVERT: A 1022 GLN cc_start: 0.8350 (mp10) cc_final: 0.7827 (mm-40) REVERT: B 515 MET cc_start: 0.5153 (pmm) cc_final: 0.4897 (pmm) REVERT: B 717 HIS cc_start: 0.8083 (m-70) cc_final: 0.7825 (m-70) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2365 time to fit residues: 51.8997 Evaluate side-chains 115 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 51 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 2 optimal weight: 0.4980 chunk 24 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 749 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.117499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.092317 restraints weight = 42882.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.094562 restraints weight = 23945.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.096048 restraints weight = 15548.284| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11438 Z= 0.182 Angle : 0.636 6.380 15446 Z= 0.337 Chirality : 0.045 0.235 1663 Planarity : 0.004 0.049 1987 Dihedral : 5.035 19.918 1504 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.22), residues: 1357 helix: 0.48 (0.24), residues: 457 sheet: -1.71 (0.35), residues: 204 loop : -1.17 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 578 HIS 0.007 0.001 HIS A1150 PHE 0.022 0.002 PHE A 952 TYR 0.031 0.002 TYR A 206 ARG 0.006 0.001 ARG B 577 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 425) hydrogen bonds : angle 5.82456 ( 1191) covalent geometry : bond 0.00402 (11438) covalent geometry : angle 0.63613 (15446) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8200 (mmm) cc_final: 0.7921 (mmm) REVERT: A 331 LEU cc_start: 0.9407 (mt) cc_final: 0.8895 (mt) REVERT: A 376 ARG cc_start: 0.7259 (mmp-170) cc_final: 0.6810 (mmm160) REVERT: A 495 TYR cc_start: 0.8085 (t80) cc_final: 0.7443 (t80) REVERT: A 592 MET cc_start: 0.1435 (ptp) cc_final: 0.1069 (ptp) REVERT: A 845 LEU cc_start: 0.8694 (tp) cc_final: 0.8214 (tp) REVERT: A 1003 TRP cc_start: 0.9002 (m-10) cc_final: 0.8420 (m-90) REVERT: B 717 HIS cc_start: 0.7880 (m-70) cc_final: 0.7594 (m-70) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2500 time to fit residues: 54.0787 Evaluate side-chains 108 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 92 optimal weight: 0.0770 chunk 129 optimal weight: 0.0870 chunk 86 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN A 723 HIS ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.121710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.096706 restraints weight = 41866.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.099103 restraints weight = 23231.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.100688 restraints weight = 14907.573| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11438 Z= 0.119 Angle : 0.627 8.159 15446 Z= 0.326 Chirality : 0.044 0.162 1663 Planarity : 0.004 0.050 1987 Dihedral : 4.809 24.559 1504 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.08 % Allowed : 1.13 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.22), residues: 1357 helix: 0.60 (0.24), residues: 460 sheet: -1.60 (0.36), residues: 195 loop : -1.10 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 578 HIS 0.004 0.001 HIS A 327 PHE 0.016 0.002 PHE A 952 TYR 0.027 0.001 TYR A 206 ARG 0.011 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 425) hydrogen bonds : angle 5.60344 ( 1191) covalent geometry : bond 0.00258 (11438) covalent geometry : angle 0.62653 (15446) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8169 (mmm) cc_final: 0.7825 (mmm) REVERT: A 304 GLU cc_start: 0.8473 (mp0) cc_final: 0.7532 (tp30) REVERT: A 331 LEU cc_start: 0.9224 (mt) cc_final: 0.8706 (mt) REVERT: A 376 ARG cc_start: 0.7157 (mmp-170) cc_final: 0.6924 (tpm170) REVERT: A 579 ARG cc_start: 0.8562 (ptm-80) cc_final: 0.8294 (tmm-80) REVERT: A 592 MET cc_start: 0.1339 (ptp) cc_final: 0.0970 (ptp) REVERT: A 845 LEU cc_start: 0.8747 (tp) cc_final: 0.8276 (tp) REVERT: A 1003 TRP cc_start: 0.8927 (m-10) cc_final: 0.8409 (m-90) REVERT: A 1141 MET cc_start: 0.8967 (pmm) cc_final: 0.8737 (pmm) REVERT: B 717 HIS cc_start: 0.7980 (m-70) cc_final: 0.7694 (m-70) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.2244 time to fit residues: 52.9323 Evaluate side-chains 113 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 10 optimal weight: 10.0000 chunk 95 optimal weight: 0.0170 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 overall best weight: 2.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 749 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.118372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.093117 restraints weight = 42311.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.095425 restraints weight = 23704.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.096961 restraints weight = 15324.887| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11438 Z= 0.165 Angle : 0.660 10.459 15446 Z= 0.346 Chirality : 0.045 0.184 1663 Planarity : 0.004 0.049 1987 Dihedral : 4.899 23.901 1504 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.22), residues: 1357 helix: 0.62 (0.24), residues: 458 sheet: -1.43 (0.37), residues: 193 loop : -1.12 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 578 HIS 0.005 0.001 HIS A1072 PHE 0.023 0.002 PHE A 952 TYR 0.025 0.002 TYR A 206 ARG 0.005 0.001 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 425) hydrogen bonds : angle 5.75576 ( 1191) covalent geometry : bond 0.00369 (11438) covalent geometry : angle 0.65963 (15446) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8225 (mmm) cc_final: 0.7919 (mmm) REVERT: A 331 LEU cc_start: 0.9313 (mt) cc_final: 0.8927 (mt) REVERT: A 376 ARG cc_start: 0.7158 (mmp-170) cc_final: 0.6746 (mmm160) REVERT: A 495 TYR cc_start: 0.8031 (t80) cc_final: 0.7489 (t80) REVERT: A 579 ARG cc_start: 0.8516 (ptm-80) cc_final: 0.7832 (tmm-80) REVERT: A 592 MET cc_start: 0.1690 (ptp) cc_final: 0.1355 (ptp) REVERT: A 845 LEU cc_start: 0.8675 (tp) cc_final: 0.8205 (tp) REVERT: A 1003 TRP cc_start: 0.8947 (m-10) cc_final: 0.8350 (m-90) REVERT: B 717 HIS cc_start: 0.8046 (m-70) cc_final: 0.7745 (m-70) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2458 time to fit residues: 53.7500 Evaluate side-chains 116 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.0670 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 6 optimal weight: 0.1980 chunk 128 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 106 optimal weight: 0.0020 overall best weight: 0.3926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 214 GLN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 HIS ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 594 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.122061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.096918 restraints weight = 41813.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.099421 restraints weight = 22954.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.101085 restraints weight = 14530.075| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11438 Z= 0.120 Angle : 0.652 8.946 15446 Z= 0.338 Chirality : 0.045 0.230 1663 Planarity : 0.004 0.050 1987 Dihedral : 4.717 24.476 1504 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.22), residues: 1357 helix: 0.62 (0.25), residues: 460 sheet: -1.53 (0.33), residues: 228 loop : -1.15 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 578 HIS 0.005 0.001 HIS A 416 PHE 0.021 0.002 PHE A 952 TYR 0.027 0.001 TYR A 206 ARG 0.005 0.001 ARG A 582 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 425) hydrogen bonds : angle 5.53882 ( 1191) covalent geometry : bond 0.00259 (11438) covalent geometry : angle 0.65235 (15446) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8237 (mmm) cc_final: 0.7939 (mmm) REVERT: A 173 ILE cc_start: 0.8646 (pt) cc_final: 0.8260 (pt) REVERT: A 304 GLU cc_start: 0.8331 (mp0) cc_final: 0.7514 (tp30) REVERT: A 331 LEU cc_start: 0.9098 (mt) cc_final: 0.8687 (mt) REVERT: A 351 MET cc_start: 0.9334 (mmm) cc_final: 0.8562 (mpp) REVERT: A 357 GLU cc_start: 0.6436 (tt0) cc_final: 0.5974 (tt0) REVERT: A 376 ARG cc_start: 0.7101 (mmp-170) cc_final: 0.6513 (mmm160) REVERT: A 592 MET cc_start: 0.1447 (ptp) cc_final: 0.1207 (ptp) REVERT: A 845 LEU cc_start: 0.8736 (tp) cc_final: 0.8275 (tp) REVERT: A 1003 TRP cc_start: 0.8856 (m-10) cc_final: 0.8321 (m-90) REVERT: A 1009 MET cc_start: 0.7164 (mmp) cc_final: 0.6942 (mmp) REVERT: A 1141 MET cc_start: 0.8824 (pmm) cc_final: 0.8552 (pmm) REVERT: B 717 HIS cc_start: 0.8052 (m-70) cc_final: 0.7769 (m-70) REVERT: B 721 LYS cc_start: 0.2815 (tttm) cc_final: 0.2609 (tmtt) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2347 time to fit residues: 54.2177 Evaluate side-chains 120 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 30 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 71 optimal weight: 0.0670 chunk 85 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 95 optimal weight: 0.0030 chunk 13 optimal weight: 0.0980 chunk 57 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.3128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 408 HIS A 723 HIS ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1031 ASN A1039 GLN B 749 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.122724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.097668 restraints weight = 41933.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.100148 restraints weight = 23191.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.101822 restraints weight = 14718.328| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3857 r_free = 0.3857 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3857 r_free = 0.3857 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11438 Z= 0.118 Angle : 0.641 9.756 15446 Z= 0.332 Chirality : 0.044 0.230 1663 Planarity : 0.004 0.050 1987 Dihedral : 4.620 23.828 1504 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.22), residues: 1357 helix: 0.63 (0.24), residues: 460 sheet: -1.48 (0.33), residues: 231 loop : -1.15 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP A 145 HIS 0.005 0.001 HIS A 455 PHE 0.033 0.002 PHE A 421 TYR 0.025 0.001 TYR A 611 ARG 0.005 0.000 ARG A 582 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 425) hydrogen bonds : angle 5.48477 ( 1191) covalent geometry : bond 0.00258 (11438) covalent geometry : angle 0.64095 (15446) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3832.65 seconds wall clock time: 68 minutes 6.57 seconds (4086.57 seconds total)