Starting phenix.real_space_refine on Sun Dec 29 19:27:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jqi_36573/12_2024/8jqi_36573_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jqi_36573/12_2024/8jqi_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_36573/12_2024/8jqi_36573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jqi_36573/12_2024/8jqi_36573.map" model { file = "/net/cci-nas-00/data/ceres_data/8jqi_36573/12_2024/8jqi_36573_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jqi_36573/12_2024/8jqi_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-5532/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: 6.37, per 1000 atoms: 0.57 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: 2.75 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: 1.47 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: 4.10 Time building geometry restraints manager: 3.20 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: 0.590 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.580 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.630 ------------------------------------------------------------------------------- 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= 0.346 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 *********************** 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 : 1.367 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: 0.2822 time to fit residues: 70.6141 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 : 1.284 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 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= 0.354 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 : 20.85 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 *********************** 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 : 1.346 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: 0.7568 (tp30) cc_final: 0.7354 (tp30) REVERT: A 331 LEU cc_start: 0.9315 (mt) cc_final: 0.8811 (mp) REVERT: A 351 MET cc_start: 0.9093 (mtp) cc_final: 0.8398 (mtp) REVERT: A 495 TYR cc_start: 0.7745 (t80) cc_final: 0.7229 (t80) REVERT: A 729 MET cc_start: 0.7936 (ppp) cc_final: 0.7657 (ppp) REVERT: A 845 LEU cc_start: 0.8712 (tp) cc_final: 0.8292 (tp) REVERT: A 1003 TRP cc_start: 0.8746 (m-90) cc_final: 0.8398 (m-90) REVERT: A 1021 MET cc_start: 0.8304 (tpp) cc_final: 0.7865 (tpp) REVERT: B 717 HIS cc_start: 0.8295 (m-70) cc_final: 0.8081 (m-70) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2443 time to fit residues: 53.1463 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 : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 123 optimal weight: 20.0000 chunk 133 optimal weight: 20.0000 chunk 110 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2071 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= 0.267 Angle : 0.633 6.466 15446 Z= 0.337 Chirality : 0.045 0.174 1663 Planarity : 0.005 0.052 1987 Dihedral : 5.191 22.118 1504 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.08 % Allowed : 4.53 % Favored : 95.39 % 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: -0.99 (0.22), residues: 1357 helix: 0.52 (0.24), residues: 457 sheet: -1.57 (0.35), residues: 203 loop : -1.13 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1003 HIS 0.005 0.001 HIS A1025 PHE 0.035 0.002 PHE A1028 TYR 0.017 0.002 TYR A 151 ARG 0.005 0.000 ARG B 577 *********************** 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 154 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 1.473 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: A 210 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7862 (mtm) REVERT: A 313 ASP cc_start: 0.8032 (m-30) cc_final: 0.7793 (m-30) REVERT: A 331 LEU cc_start: 0.9349 (mt) cc_final: 0.8779 (mt) REVERT: A 351 MET cc_start: 0.8889 (mtp) cc_final: 0.8334 (mtp) REVERT: A 415 ARG cc_start: 0.7595 (mtt-85) cc_final: 0.6650 (mtm110) REVERT: A 495 TYR cc_start: 0.7756 (t80) cc_final: 0.7126 (t80) REVERT: A 729 MET cc_start: 0.7780 (ppp) cc_final: 0.7558 (ppp) REVERT: A 845 LEU cc_start: 0.8707 (tp) cc_final: 0.8298 (tp) REVERT: A 1003 TRP cc_start: 0.8860 (m-90) cc_final: 0.8415 (m-90) REVERT: A 1072 HIS cc_start: 0.7249 (m90) cc_final: 0.7018 (m170) REVERT: B 515 MET cc_start: 0.3311 (pmm) cc_final: 0.3057 (pmm) REVERT: B 532 MET cc_start: -0.3643 (mtm) cc_final: -0.3895 (ptp) REVERT: B 717 HIS cc_start: 0.8253 (m-70) cc_final: 0.8024 (m-70) outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.2586 time to fit residues: 56.5380 Evaluate side-chains 118 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 59 optimal weight: 0.0470 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 109 optimal weight: 30.0000 overall best weight: 0.9680 ------------------------------------------------------------------------------- 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 990 GLN ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2455 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= 0.170 Angle : 0.582 9.427 15446 Z= 0.304 Chirality : 0.044 0.204 1663 Planarity : 0.004 0.048 1987 Dihedral : 4.829 19.657 1504 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % 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: -0.73 (0.22), residues: 1357 helix: 0.74 (0.24), residues: 459 sheet: -1.44 (0.36), residues: 196 loop : -0.99 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 578 HIS 0.004 0.001 HIS A 723 PHE 0.021 0.002 PHE A 952 TYR 0.029 0.001 TYR A 206 ARG 0.005 0.000 ARG A 700 *********************** 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 159 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.320 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: A 47 MET cc_start: 0.8195 (mmm) cc_final: 0.7962 (mmm) REVERT: A 173 ILE cc_start: 0.8274 (pt) cc_final: 0.8066 (pt) REVERT: A 313 ASP cc_start: 0.8013 (m-30) cc_final: 0.7796 (m-30) REVERT: A 331 LEU cc_start: 0.9244 (mt) cc_final: 0.8775 (mt) REVERT: A 351 MET cc_start: 0.8893 (mtp) cc_final: 0.8201 (mtp) REVERT: A 495 TYR cc_start: 0.7804 (t80) cc_final: 0.7160 (t80) REVERT: A 845 LEU cc_start: 0.8747 (tp) cc_final: 0.8284 (tp) REVERT: A 1003 TRP cc_start: 0.8841 (m-10) cc_final: 0.8459 (m-90) REVERT: B 515 MET cc_start: 0.3636 (pmm) cc_final: 0.3403 (pmm) REVERT: B 583 TYR cc_start: 0.5672 (m-80) cc_final: 0.5297 (p90) REVERT: B 717 HIS cc_start: 0.8264 (m-70) cc_final: 0.8035 (m-70) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2573 time to fit residues: 59.7678 Evaluate side-chains 118 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 117 optimal weight: 0.0670 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.5924 ------------------------------------------------------------------------------- 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 571 ASN ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11438 Z= 0.191 Angle : 0.584 7.700 15446 Z= 0.307 Chirality : 0.043 0.152 1663 Planarity : 0.004 0.051 1987 Dihedral : 4.741 19.190 1504 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.08 % Allowed : 2.59 % Favored : 97.33 % 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: -0.67 (0.22), residues: 1357 helix: 0.80 (0.24), residues: 459 sheet: -1.39 (0.36), residues: 196 loop : -0.96 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 578 HIS 0.008 0.001 HIS A 203 PHE 0.021 0.002 PHE A 952 TYR 0.031 0.002 TYR A 206 ARG 0.006 0.000 ARG A 564 *********************** 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 157 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 1.334 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: A 47 MET cc_start: 0.8175 (mmm) cc_final: 0.7944 (mmm) REVERT: A 173 ILE cc_start: 0.8377 (pt) cc_final: 0.8125 (pt) REVERT: A 304 GLU cc_start: 0.7393 (tp30) cc_final: 0.7165 (tp30) REVERT: A 331 LEU cc_start: 0.9263 (mt) cc_final: 0.8747 (mt) REVERT: A 376 ARG cc_start: 0.7146 (mmp-170) cc_final: 0.6853 (tpm170) REVERT: A 415 ARG cc_start: 0.7592 (mtt-85) cc_final: 0.6934 (mtm110) REVERT: A 495 TYR cc_start: 0.7839 (t80) cc_final: 0.7189 (t80) REVERT: A 592 MET cc_start: 0.1324 (ptp) cc_final: 0.1064 (ptp) REVERT: A 728 LYS cc_start: 0.8472 (tptp) cc_final: 0.8266 (tptp) REVERT: A 845 LEU cc_start: 0.8763 (tp) cc_final: 0.8260 (tp) REVERT: A 1003 TRP cc_start: 0.8912 (m-10) cc_final: 0.8411 (m-90) REVERT: B 515 MET cc_start: 0.4181 (pmm) cc_final: 0.3836 (pmm) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.2723 time to fit residues: 60.4983 Evaluate side-chains 118 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 32 optimal weight: 0.0980 chunk 131 optimal weight: 20.0000 chunk 109 optimal weight: 30.0000 chunk 60 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 637 ASN ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11438 Z= 0.278 Angle : 0.638 6.753 15446 Z= 0.338 Chirality : 0.046 0.330 1663 Planarity : 0.005 0.050 1987 Dihedral : 5.000 19.397 1504 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: -0.90 (0.22), residues: 1357 helix: 0.61 (0.24), residues: 456 sheet: -1.51 (0.36), residues: 199 loop : -1.09 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1003 HIS 0.003 0.001 HIS B 589 PHE 0.023 0.002 PHE A 952 TYR 0.019 0.002 TYR A 206 ARG 0.006 0.001 ARG A 347 *********************** 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 158 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.282 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: 0.8163 (mmm) cc_final: 0.7877 (mmm) REVERT: A 173 ILE cc_start: 0.8537 (pt) cc_final: 0.8336 (pt) REVERT: A 304 GLU cc_start: 0.7496 (tp30) cc_final: 0.7294 (tp30) REVERT: A 331 LEU cc_start: 0.9344 (mt) cc_final: 0.8820 (mt) REVERT: A 376 ARG cc_start: 0.7230 (mmp-170) cc_final: 0.6833 (mmm160) REVERT: A 495 TYR cc_start: 0.7852 (t80) cc_final: 0.7165 (t80) REVERT: A 592 MET cc_start: 0.1517 (ptp) cc_final: 0.1259 (ptp) REVERT: A 728 LYS cc_start: 0.8547 (tptp) cc_final: 0.8304 (tptp) REVERT: A 845 LEU cc_start: 0.8712 (tp) cc_final: 0.8253 (tp) REVERT: A 1003 TRP cc_start: 0.9002 (m-10) cc_final: 0.8453 (m-90) REVERT: A 1022 GLN cc_start: 0.8564 (mp10) cc_final: 0.8337 (mp10) REVERT: B 515 MET cc_start: 0.4508 (pmm) cc_final: 0.4304 (pmm) REVERT: B 653 TYR cc_start: 0.7154 (m-10) cc_final: 0.6631 (m-10) REVERT: B 675 ARG cc_start: 0.7806 (mtt180) cc_final: 0.7311 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2770 time to fit residues: 60.8220 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 : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 chunk 82 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 HIS ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11438 Z= 0.322 Angle : 0.690 7.165 15446 Z= 0.367 Chirality : 0.047 0.285 1663 Planarity : 0.005 0.048 1987 Dihedral : 5.287 20.446 1504 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % 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: -1.12 (0.22), residues: 1357 helix: 0.36 (0.24), residues: 456 sheet: -1.63 (0.35), residues: 204 loop : -1.18 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 374 HIS 0.005 0.001 HIS A1025 PHE 0.024 0.002 PHE A 952 TYR 0.020 0.002 TYR A 206 ARG 0.010 0.001 ARG B 577 *********************** 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 149 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.425 Fit side-chains 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: 0.7837 (mmm) REVERT: A 103 GLN cc_start: 0.8177 (mp10) cc_final: 0.7920 (mp10) REVERT: A 187 PHE cc_start: 0.8219 (m-10) cc_final: 0.7987 (m-80) REVERT: A 210 MET cc_start: 0.8110 (mtm) cc_final: 0.7808 (mtm) REVERT: A 305 LYS cc_start: 0.8847 (ptpp) cc_final: 0.8509 (ptpp) REVERT: A 331 LEU cc_start: 0.9438 (mt) cc_final: 0.8964 (mt) REVERT: A 376 ARG cc_start: 0.7299 (mmp-170) cc_final: 0.6852 (mmm160) REVERT: A 495 TYR cc_start: 0.8061 (t80) cc_final: 0.7435 (t80) REVERT: A 845 LEU cc_start: 0.8668 (tp) cc_final: 0.8193 (tp) REVERT: A 905 GLU cc_start: 0.8583 (mp0) cc_final: 0.8370 (mp0) REVERT: A 1003 TRP cc_start: 0.8893 (m-10) cc_final: 0.8364 (m-90) REVERT: B 653 TYR cc_start: 0.7078 (m-10) cc_final: 0.6622 (m-10) REVERT: B 675 ARG cc_start: 0.7884 (mtt180) cc_final: 0.7369 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2607 time to fit residues: 55.3435 Evaluate side-chains 112 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 119 optimal weight: 0.9990 chunk 125 optimal weight: 0.0570 chunk 114 optimal weight: 5.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 594 GLN ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11438 Z= 0.168 Angle : 0.633 7.484 15446 Z= 0.330 Chirality : 0.044 0.165 1663 Planarity : 0.004 0.049 1987 Dihedral : 4.847 20.993 1504 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: -0.90 (0.22), residues: 1357 helix: 0.59 (0.24), residues: 461 sheet: -1.44 (0.37), residues: 187 loop : -1.13 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 578 HIS 0.005 0.001 HIS A 455 PHE 0.018 0.002 PHE A 952 TYR 0.032 0.001 TYR A 206 ARG 0.006 0.000 ARG B 577 *********************** 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 159 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.259 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: 0.7809 (mmm) REVERT: A 173 ILE cc_start: 0.8657 (pt) cc_final: 0.8437 (pt) REVERT: A 331 LEU cc_start: 0.9286 (mt) cc_final: 0.8702 (mt) REVERT: A 376 ARG cc_start: 0.7244 (mmp-170) cc_final: 0.6955 (tpm170) REVERT: A 592 MET cc_start: 0.1542 (ptp) cc_final: 0.1338 (ptp) REVERT: A 845 LEU cc_start: 0.8755 (tp) cc_final: 0.8270 (tp) REVERT: A 1003 TRP cc_start: 0.8886 (m-10) cc_final: 0.8402 (m-90) REVERT: A 1022 GLN cc_start: 0.8251 (mp10) cc_final: 0.7653 (mm-40) REVERT: A 1141 MET cc_start: 0.8956 (pmm) cc_final: 0.8737 (pmm) REVERT: B 515 MET cc_start: 0.5193 (pmm) cc_final: 0.4675 (pmm) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2478 time to fit residues: 56.5236 Evaluate side-chains 117 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 53 optimal weight: 0.0470 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 110 optimal weight: 0.4980 chunk 115 optimal weight: 0.2980 chunk 121 optimal weight: 4.9990 chunk 80 optimal weight: 0.0670 chunk 129 optimal weight: 9.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 723 HIS ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11438 Z= 0.174 Angle : 0.639 8.367 15446 Z= 0.334 Chirality : 0.045 0.170 1663 Planarity : 0.004 0.050 1987 Dihedral : 4.729 25.585 1504 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: 0.55 (0.24), residues: 461 sheet: -1.40 (0.35), residues: 215 loop : -1.13 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 578 HIS 0.005 0.001 HIS A 416 PHE 0.031 0.002 PHE A 421 TYR 0.031 0.001 TYR A 206 ARG 0.012 0.001 ARG A 579 *********************** 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 158 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.398 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: 0.8124 (mmm) cc_final: 0.7834 (mmm) REVERT: A 173 ILE cc_start: 0.8593 (pt) cc_final: 0.8374 (pt) REVERT: A 194 LYS cc_start: 0.8442 (ptmt) cc_final: 0.8204 (mptt) REVERT: A 331 LEU cc_start: 0.9230 (mt) cc_final: 0.8758 (mt) REVERT: A 376 ARG cc_start: 0.7144 (mmp-170) cc_final: 0.6933 (tpm170) REVERT: A 845 LEU cc_start: 0.8747 (tp) cc_final: 0.8281 (tp) REVERT: A 1003 TRP cc_start: 0.8865 (m-10) cc_final: 0.8372 (m-90) REVERT: A 1141 MET cc_start: 0.8825 (pmm) cc_final: 0.8578 (pmm) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2711 time to fit residues: 61.0568 Evaluate side-chains 121 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 11 optimal weight: 0.5980 chunk 83 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 114 optimal weight: 8.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3739 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= 0.186 Angle : 0.640 9.712 15446 Z= 0.335 Chirality : 0.045 0.226 1663 Planarity : 0.004 0.050 1987 Dihedral : 4.703 25.543 1504 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 0.57 (0.24), residues: 460 sheet: -1.32 (0.35), residues: 215 loop : -1.16 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 578 HIS 0.004 0.001 HIS A1150 PHE 0.031 0.002 PHE A 421 TYR 0.023 0.001 TYR A 206 ARG 0.004 0.000 ARG B 577 ********************** 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 151 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.407 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: 0.8129 (mmm) cc_final: 0.7847 (mmm) REVERT: A 331 LEU cc_start: 0.9159 (mt) cc_final: 0.8733 (mt) REVERT: A 376 ARG cc_start: 0.7107 (mmp-170) cc_final: 0.6522 (mmm160) REVERT: A 417 MET cc_start: 0.8006 (ttp) cc_final: 0.7701 (ptm) REVERT: A 845 LEU cc_start: 0.8688 (tp) cc_final: 0.8217 (tp) REVERT: A 1003 TRP cc_start: 0.8881 (m-10) cc_final: 0.8348 (m-90) REVERT: A 1141 MET cc_start: 0.8800 (pmm) cc_final: 0.8553 (pmm) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2585 time to fit residues: 56.2395 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 : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 110 optimal weight: 0.0170 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 723 HIS ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 ASN ** 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 = 0.4218 r_free = 0.4218 target = 0.121759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.096748 restraints weight = 41892.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.099230 restraints weight = 23091.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.100855 restraints weight = 14718.116| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3832 r_free = 0.3832 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11438 Z= 0.173 Angle : 0.638 10.236 15446 Z= 0.334 Chirality : 0.045 0.230 1663 Planarity : 0.004 0.049 1987 Dihedral : 4.597 24.325 1504 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 0.60 (0.24), residues: 459 sheet: -1.32 (0.35), residues: 215 loop : -1.12 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 578 HIS 0.010 0.001 HIS A 130 PHE 0.031 0.002 PHE A 421 TYR 0.024 0.001 TYR A 206 ARG 0.004 0.000 ARG B 577 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2306.78 seconds wall clock time: 43 minutes 43.96 seconds (2623.96 seconds total)