Starting phenix.real_space_refine on Wed Feb 12 11:57:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w7w_32350/02_2025/7w7w_32350.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w7w_32350/02_2025/7w7w_32350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w7w_32350/02_2025/7w7w_32350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w7w_32350/02_2025/7w7w_32350.map" model { file = "/net/cci-nas-00/data/ceres_data/7w7w_32350/02_2025/7w7w_32350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w7w_32350/02_2025/7w7w_32350.cif" } resolution = 3.2 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= -0.000 sd= 0.011 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 58 5.16 5 C 5011 2.51 5 N 1315 2.21 5 O 1480 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7870 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 7864 Classifications: {'peptide': 1018} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 46, 'TRANS': 971} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.50, per 1000 atoms: 0.57 Number of scatterers: 7870 At special positions: 0 Unit cell: (99.935, 92.345, 136.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 58 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1480 8.00 N 1315 7.00 C 5011 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 875 " - pdb=" SG CYS A 887 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 924.7 milliseconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 6 sheets defined 53.1% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 8 through 17 removed outlier: 3.617A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 37 removed outlier: 3.833A pdb=" N LYS A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 59 through 79 removed outlier: 3.615A pdb=" N PHE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 87 Processing helix chain 'A' and resid 88 through 110 Processing helix chain 'A' and resid 141 through 145 removed outlier: 3.865A pdb=" N ASP A 144 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE A 145 " --> pdb=" O ALA A 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 141 through 145' Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 226 through 229 Processing helix chain 'A' and resid 230 through 241 Processing helix chain 'A' and resid 247 through 279 removed outlier: 3.778A pdb=" N GLY A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 307 removed outlier: 4.071A pdb=" N ALA A 292 " --> pdb=" O TRP A 288 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 329 removed outlier: 4.661A pdb=" N ALA A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 407 through 420 removed outlier: 3.617A pdb=" N VAL A 411 " --> pdb=" O TYR A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 452 removed outlier: 3.592A pdb=" N MET A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 removed outlier: 3.717A pdb=" N ALA A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 removed outlier: 3.624A pdb=" N LEU A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 523 Processing helix chain 'A' and resid 537 through 553 Processing helix chain 'A' and resid 580 through 587 removed outlier: 3.946A pdb=" N ILE A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 616 removed outlier: 3.727A pdb=" N SER A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 Processing helix chain 'A' and resid 654 through 659 removed outlier: 3.675A pdb=" N GLU A 659 " --> pdb=" O ARG A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 672 removed outlier: 3.958A pdb=" N CYS A 669 " --> pdb=" O GLN A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 693 removed outlier: 3.658A pdb=" N PHE A 693 " --> pdb=" O PHE A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 723 through 729 Processing helix chain 'A' and resid 739 through 781 removed outlier: 4.103A pdb=" N VAL A 743 " --> pdb=" O PHE A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 808 removed outlier: 3.810A pdb=" N THR A 798 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASP A 799 " --> pdb=" O ASN A 795 " (cutoff:3.500A) Proline residue: A 802 - end of helix Processing helix chain 'A' and resid 829 through 857 removed outlier: 3.530A pdb=" N PHE A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 870 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.575A pdb=" N ILE A 889 " --> pdb=" O ASP A 886 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 890 " --> pdb=" O CYS A 887 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 891 " --> pdb=" O ALA A 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 891' Processing helix chain 'A' and resid 892 through 913 removed outlier: 4.287A pdb=" N MET A 896 " --> pdb=" O SER A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 928 Processing helix chain 'A' and resid 929 through 949 removed outlier: 3.743A pdb=" N VAL A 933 " --> pdb=" O ASN A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 956 removed outlier: 3.935A pdb=" N ILE A 955 " --> pdb=" O PRO A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 974 Processing helix chain 'A' and resid 974 through 989 removed outlier: 4.044A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1031 removed outlier: 3.626A pdb=" N ILE A1022 " --> pdb=" O PHE A1018 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A1023 " --> pdb=" O VAL A1019 " (cutoff:3.500A) Proline residue: A1024 - end of helix removed outlier: 3.536A pdb=" N ILE A1027 " --> pdb=" O MET A1023 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP A1028 " --> pdb=" O PRO A1024 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 153 removed outlier: 7.037A pdb=" N MET A 220 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASP A 162 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 188 removed outlier: 6.183A pdb=" N ASP A 176 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ILE A 214 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 331 through 333 removed outlier: 6.577A pdb=" N GLY A 716 " --> pdb=" O MET A 732 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU A 734 " --> pdb=" O GLY A 716 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ALA A 718 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N THR A 697 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE A 717 " --> pdb=" O THR A 697 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N MET A 699 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N MET A 719 " --> pdb=" O MET A 699 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N GLY A 701 " --> pdb=" O MET A 719 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE A 348 " --> pdb=" O ILE A 621 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE A 623 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N SER A 350 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N PHE A 675 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N MET A 622 " --> pdb=" O PHE A 675 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396 removed outlier: 3.782A pdb=" N ARG A 371 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASN A 380 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU A 369 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N PHE A 382 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N PHE A 367 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 384 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ARG A 365 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N VAL A 363 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 599 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 369 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N VAL A 593 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 14.294A pdb=" N ARG A 371 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 15.747A pdb=" N THR A 591 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N PHE A 592 " --> pdb=" O THR A 565 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR A 565 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 594 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A 483 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR A 499 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS A 481 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 396 removed outlier: 3.782A pdb=" N ARG A 371 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASN A 380 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU A 369 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N PHE A 382 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N PHE A 367 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 384 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ARG A 365 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N VAL A 363 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 599 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 369 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N VAL A 593 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 14.294A pdb=" N ARG A 371 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 15.747A pdb=" N THR A 591 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N CYS A 524 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE A 592 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N HIS A 526 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N GLY A 594 " --> pdb=" O HIS A 526 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ARG A 528 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 12.822A pdb=" N VAL A 596 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 427 removed outlier: 3.562A pdb=" N ASP A 426 " --> pdb=" O GLU A 435 " (cutoff:3.500A) 411 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: 2.70 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2561 1.34 - 1.46: 1086 1.46 - 1.58: 4276 1.58 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 8017 Sorted by residual: bond pdb=" F1 ALF A2001 " pdb="AL ALF A2001 " ideal model delta sigma weight residual 1.684 1.783 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" F2 ALF A2001 " pdb="AL ALF A2001 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" F3 ALF A2001 " pdb="AL ALF A2001 " ideal model delta sigma weight residual 1.685 1.782 -0.097 2.00e-02 2.50e+03 2.38e+01 bond pdb=" F4 ALF A2001 " pdb="AL ALF A2001 " ideal model delta sigma weight residual 1.686 1.783 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" N LEU A 796 " pdb=" CA LEU A 796 " ideal model delta sigma weight residual 1.468 1.455 0.014 1.24e-02 6.50e+03 1.20e+00 ... (remaining 8012 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.20: 10876 14.20 - 28.40: 4 28.40 - 42.60: 0 42.60 - 56.80: 0 56.80 - 71.00: 2 Bond angle restraints: 10882 Sorted by residual: angle pdb=" F1 ALF A2001 " pdb="AL ALF A2001 " pdb=" F2 ALF A2001 " ideal model delta sigma weight residual 108.68 179.68 -71.00 3.00e+00 1.11e-01 5.60e+02 angle pdb=" F3 ALF A2001 " pdb="AL ALF A2001 " pdb=" F4 ALF A2001 " ideal model delta sigma weight residual 109.63 179.93 -70.30 3.00e+00 1.11e-01 5.49e+02 angle pdb=" F2 ALF A2001 " pdb="AL ALF A2001 " pdb=" F4 ALF A2001 " ideal model delta sigma weight residual 110.21 90.17 20.04 3.00e+00 1.11e-01 4.46e+01 angle pdb=" F2 ALF A2001 " pdb="AL ALF A2001 " pdb=" F3 ALF A2001 " ideal model delta sigma weight residual 109.59 89.78 19.81 3.00e+00 1.11e-01 4.36e+01 angle pdb=" F1 ALF A2001 " pdb="AL ALF A2001 " pdb=" F3 ALF A2001 " ideal model delta sigma weight residual 109.69 89.90 19.79 3.00e+00 1.11e-01 4.35e+01 ... (remaining 10877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 4394 18.01 - 36.03: 402 36.03 - 54.04: 54 54.04 - 72.06: 9 72.06 - 90.07: 3 Dihedral angle restraints: 4862 sinusoidal: 1919 harmonic: 2943 Sorted by residual: dihedral pdb=" CB CYS A 875 " pdb=" SG CYS A 875 " pdb=" SG CYS A 887 " pdb=" CB CYS A 887 " ideal model delta sinusoidal sigma weight residual -86.00 -176.07 90.07 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CA ASP A 157 " pdb=" CB ASP A 157 " pdb=" CG ASP A 157 " pdb=" OD1 ASP A 157 " ideal model delta sinusoidal sigma weight residual -30.00 -84.22 54.22 1 2.00e+01 2.50e-03 9.97e+00 dihedral pdb=" CA ILE A 116 " pdb=" C ILE A 116 " pdb=" N GLU A 117 " pdb=" CA GLU A 117 " ideal model delta harmonic sigma weight residual 180.00 -164.40 -15.60 0 5.00e+00 4.00e-02 9.74e+00 ... (remaining 4859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 880 0.037 - 0.073: 276 0.073 - 0.110: 103 0.110 - 0.147: 15 0.147 - 0.183: 2 Chirality restraints: 1276 Sorted by residual: chirality pdb=" CB ILE A 715 " pdb=" CA ILE A 715 " pdb=" CG1 ILE A 715 " pdb=" CG2 ILE A 715 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.41e-01 chirality pdb=" CA PHE A 759 " pdb=" N PHE A 759 " pdb=" C PHE A 759 " pdb=" CB PHE A 759 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA ILE A 623 " pdb=" N ILE A 623 " pdb=" C ILE A 623 " pdb=" CB ILE A 623 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 1273 not shown) Planarity restraints: 1387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 534 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO A 535 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 535 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 535 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 796 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C LEU A 796 " -0.032 2.00e-02 2.50e+03 pdb=" O LEU A 796 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL A 797 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 959 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO A 960 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 960 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 960 " 0.023 5.00e-02 4.00e+02 ... (remaining 1384 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 55 2.62 - 3.19: 7143 3.19 - 3.76: 12450 3.76 - 4.33: 16583 4.33 - 4.90: 27875 Nonbonded interactions: 64106 Sorted by model distance: nonbonded pdb=" OD2 ASP A 351 " pdb="MG MG A2002 " model vdw 2.051 2.170 nonbonded pdb=" F3 ALF A2001 " pdb="MG MG A2002 " model vdw 2.055 2.120 nonbonded pdb=" OD1 ASP A 702 " pdb="MG MG A2002 " model vdw 2.064 2.170 nonbonded pdb=" O THR A 353 " pdb="MG MG A2002 " model vdw 2.071 2.170 nonbonded pdb=" NH2 ARG A 131 " pdb=" OE1 GLU A 152 " model vdw 2.167 3.120 ... (remaining 64101 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.430 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.260 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 8017 Z= 0.216 Angle : 1.162 71.002 10882 Z= 0.455 Chirality : 0.041 0.183 1276 Planarity : 0.004 0.055 1387 Dihedral : 13.443 75.289 2951 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 0.82 (0.26), residues: 1014 helix: 1.66 (0.24), residues: 489 sheet: -0.03 (0.50), residues: 105 loop : -0.62 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 831 HIS 0.002 0.001 HIS A 943 PHE 0.019 0.001 PHE A 759 TYR 0.025 0.001 TYR A 586 ARG 0.005 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 452 MET cc_start: 0.6826 (ptt) cc_final: 0.6150 (ptt) REVERT: A 557 THR cc_start: 0.7993 (p) cc_final: 0.7663 (p) REVERT: A 784 GLU cc_start: 0.5533 (mm-30) cc_final: 0.4672 (mm-30) REVERT: A 1023 MET cc_start: 0.1857 (mmt) cc_final: 0.1158 (mmt) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2051 time to fit residues: 35.1241 Evaluate side-chains 98 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 8.9990 chunk 76 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 0.0770 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 738 ASN A 879 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.179664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.144273 restraints weight = 8674.268| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.78 r_work: 0.3537 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8017 Z= 0.240 Angle : 0.841 30.847 10882 Z= 0.362 Chirality : 0.044 0.175 1276 Planarity : 0.005 0.044 1387 Dihedral : 4.302 15.287 1078 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.03 % Allowed : 7.47 % Favored : 91.49 % 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: 0.58 (0.26), residues: 1014 helix: 1.44 (0.23), residues: 497 sheet: -0.19 (0.52), residues: 96 loop : -0.72 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 854 HIS 0.004 0.001 HIS A 278 PHE 0.032 0.002 PHE A 759 TYR 0.012 0.001 TYR A 434 ARG 0.003 0.000 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 452 MET cc_start: 0.7102 (ptt) cc_final: 0.6525 (ptt) REVERT: A 536 MET cc_start: 0.7781 (tpp) cc_final: 0.7508 (tpt) REVERT: A 557 THR cc_start: 0.8073 (p) cc_final: 0.7747 (p) REVERT: A 758 GLN cc_start: 0.7615 (mt0) cc_final: 0.6538 (mm110) REVERT: A 784 GLU cc_start: 0.6095 (mm-30) cc_final: 0.5144 (mm-30) REVERT: A 940 MET cc_start: 0.7383 (tpp) cc_final: 0.7121 (mmm) REVERT: A 1023 MET cc_start: 0.1856 (mmt) cc_final: 0.1129 (mmt) outliers start: 9 outliers final: 7 residues processed: 110 average time/residue: 0.1902 time to fit residues: 29.3124 Evaluate side-chains 102 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 738 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 48 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.171865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.135712 restraints weight = 8890.208| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.82 r_work: 0.3430 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.121 8017 Z= 0.447 Angle : 0.925 35.302 10882 Z= 0.418 Chirality : 0.049 0.255 1276 Planarity : 0.006 0.053 1387 Dihedral : 4.891 17.897 1078 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.07 % Allowed : 12.18 % Favored : 85.75 % 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: -0.06 (0.26), residues: 1014 helix: 0.86 (0.23), residues: 492 sheet: -0.91 (0.50), residues: 98 loop : -0.82 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 36 HIS 0.005 0.001 HIS A 566 PHE 0.032 0.002 PHE A 759 TYR 0.020 0.003 TYR A 434 ARG 0.009 0.001 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.911 Fit side-chains REVERT: A 11 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6942 (mm-30) REVERT: A 439 GLU cc_start: 0.7561 (tp30) cc_final: 0.7305 (mm-30) REVERT: A 452 MET cc_start: 0.7377 (ptt) cc_final: 0.7121 (ptt) REVERT: A 575 MET cc_start: 0.6720 (mmm) cc_final: 0.6417 (tpp) REVERT: A 715 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.7709 (tp) REVERT: A 784 GLU cc_start: 0.6275 (mm-30) cc_final: 0.5222 (mm-30) REVERT: A 792 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7771 (mm) REVERT: A 836 TYR cc_start: 0.7827 (m-80) cc_final: 0.7593 (m-80) REVERT: A 1023 MET cc_start: 0.1163 (mmt) cc_final: 0.0454 (mmt) outliers start: 18 outliers final: 14 residues processed: 117 average time/residue: 0.1919 time to fit residues: 31.9059 Evaluate side-chains 118 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 969 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 75 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 68 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.175296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.140894 restraints weight = 8718.603| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.68 r_work: 0.3505 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8017 Z= 0.227 Angle : 0.832 30.910 10882 Z= 0.357 Chirality : 0.043 0.168 1276 Planarity : 0.005 0.052 1387 Dihedral : 4.449 16.448 1078 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.18 % Allowed : 14.25 % Favored : 83.56 % 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: 0.18 (0.26), residues: 1014 helix: 1.19 (0.23), residues: 491 sheet: -0.91 (0.51), residues: 97 loop : -0.85 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 831 HIS 0.003 0.001 HIS A 566 PHE 0.028 0.001 PHE A 759 TYR 0.011 0.001 TYR A 122 ARG 0.002 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.888 Fit side-chains REVERT: A 373 GLU cc_start: 0.5518 (OUTLIER) cc_final: 0.4971 (mm-30) REVERT: A 439 GLU cc_start: 0.7445 (tp30) cc_final: 0.7198 (mm-30) REVERT: A 452 MET cc_start: 0.7386 (ptt) cc_final: 0.7185 (ptt) REVERT: A 492 LYS cc_start: 0.7872 (mtpp) cc_final: 0.7532 (mtpt) REVERT: A 715 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.7707 (tp) REVERT: A 784 GLU cc_start: 0.6113 (mm-30) cc_final: 0.5026 (mm-30) REVERT: A 1023 MET cc_start: 0.1186 (mmt) cc_final: 0.0424 (mmt) outliers start: 19 outliers final: 12 residues processed: 115 average time/residue: 0.1735 time to fit residues: 28.6604 Evaluate side-chains 115 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 980 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 67 optimal weight: 0.6980 chunk 81 optimal weight: 0.0060 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.179381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.144251 restraints weight = 8685.552| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.78 r_work: 0.3532 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8017 Z= 0.162 Angle : 0.809 29.773 10882 Z= 0.341 Chirality : 0.041 0.162 1276 Planarity : 0.004 0.049 1387 Dihedral : 4.104 15.682 1078 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.18 % Allowed : 15.17 % Favored : 82.64 % 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: 0.40 (0.27), residues: 1014 helix: 1.33 (0.24), residues: 504 sheet: -0.79 (0.50), residues: 104 loop : -0.76 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 831 HIS 0.003 0.001 HIS A 566 PHE 0.029 0.001 PHE A 759 TYR 0.047 0.002 TYR A 586 ARG 0.002 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.858 Fit side-chains REVERT: A 296 PHE cc_start: 0.7744 (m-10) cc_final: 0.7459 (m-80) REVERT: A 373 GLU cc_start: 0.5741 (OUTLIER) cc_final: 0.5346 (mm-30) REVERT: A 439 GLU cc_start: 0.7454 (tp30) cc_final: 0.7232 (mm-30) REVERT: A 452 MET cc_start: 0.7286 (ptt) cc_final: 0.6955 (ptt) REVERT: A 492 LYS cc_start: 0.7879 (mtpp) cc_final: 0.7610 (mtpt) REVERT: A 599 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7215 (pt) REVERT: A 715 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.7721 (tp) REVERT: A 758 GLN cc_start: 0.7689 (mt0) cc_final: 0.6815 (tp40) REVERT: A 784 GLU cc_start: 0.6169 (mm-30) cc_final: 0.5055 (mm-30) REVERT: A 1023 MET cc_start: 0.1214 (mmt) cc_final: 0.0440 (mmt) outliers start: 19 outliers final: 12 residues processed: 124 average time/residue: 0.1834 time to fit residues: 32.0061 Evaluate side-chains 120 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 980 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 7 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.176880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.141271 restraints weight = 8698.660| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.81 r_work: 0.3500 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8017 Z= 0.226 Angle : 0.828 31.229 10882 Z= 0.353 Chirality : 0.042 0.168 1276 Planarity : 0.005 0.050 1387 Dihedral : 4.196 16.006 1078 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.22 % Allowed : 15.98 % Favored : 80.80 % 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: 0.38 (0.27), residues: 1014 helix: 1.28 (0.24), residues: 505 sheet: -0.84 (0.50), residues: 104 loop : -0.69 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 36 HIS 0.003 0.001 HIS A 566 PHE 0.027 0.001 PHE A 759 TYR 0.036 0.002 TYR A 586 ARG 0.002 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.848 Fit side-chains REVERT: A 11 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6874 (mm-30) REVERT: A 373 GLU cc_start: 0.5583 (OUTLIER) cc_final: 0.5290 (mm-30) REVERT: A 452 MET cc_start: 0.7269 (ptt) cc_final: 0.6934 (ptt) REVERT: A 467 ARG cc_start: 0.6664 (tmt170) cc_final: 0.6138 (tpt90) REVERT: A 492 LYS cc_start: 0.7904 (mtpp) cc_final: 0.7619 (mtpt) REVERT: A 599 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7218 (pt) REVERT: A 715 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.7762 (tp) REVERT: A 731 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: A 758 GLN cc_start: 0.7660 (mt0) cc_final: 0.6935 (tp40) REVERT: A 784 GLU cc_start: 0.6197 (mm-30) cc_final: 0.5068 (mm-30) REVERT: A 1023 MET cc_start: 0.1740 (mmt) cc_final: 0.0662 (mtp) outliers start: 28 outliers final: 20 residues processed: 122 average time/residue: 0.1776 time to fit residues: 31.0338 Evaluate side-chains 125 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 980 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.176925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.141483 restraints weight = 8718.109| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.80 r_work: 0.3503 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8017 Z= 0.213 Angle : 0.823 30.602 10882 Z= 0.349 Chirality : 0.042 0.168 1276 Planarity : 0.004 0.051 1387 Dihedral : 4.163 15.810 1078 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.33 % Allowed : 15.63 % Favored : 81.03 % 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: 0.40 (0.27), residues: 1014 helix: 1.31 (0.24), residues: 504 sheet: -0.74 (0.51), residues: 99 loop : -0.72 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 831 HIS 0.003 0.001 HIS A 566 PHE 0.028 0.001 PHE A 759 TYR 0.030 0.002 TYR A 586 ARG 0.004 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.861 Fit side-chains REVERT: A 11 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6872 (mm-30) REVERT: A 373 GLU cc_start: 0.5563 (OUTLIER) cc_final: 0.5331 (mm-30) REVERT: A 452 MET cc_start: 0.7202 (ptt) cc_final: 0.6855 (ptt) REVERT: A 492 LYS cc_start: 0.7804 (mtpp) cc_final: 0.7544 (mtpt) REVERT: A 599 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7209 (pt) REVERT: A 715 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7314 (tp) REVERT: A 731 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7573 (mt-10) REVERT: A 758 GLN cc_start: 0.7665 (mt0) cc_final: 0.6938 (tp40) REVERT: A 784 GLU cc_start: 0.6193 (mm-30) cc_final: 0.5077 (mm-30) REVERT: A 1023 MET cc_start: 0.1469 (mmt) cc_final: 0.0508 (mtp) outliers start: 29 outliers final: 22 residues processed: 123 average time/residue: 0.1896 time to fit residues: 33.0946 Evaluate side-chains 127 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 980 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 72 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 81 optimal weight: 0.0020 chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 61 optimal weight: 0.0670 chunk 83 optimal weight: 0.7980 overall best weight: 0.5326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.180548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.145841 restraints weight = 8657.864| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.76 r_work: 0.3565 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8017 Z= 0.154 Angle : 0.806 29.544 10882 Z= 0.336 Chirality : 0.041 0.162 1276 Planarity : 0.005 0.060 1387 Dihedral : 3.918 15.259 1078 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.64 % Allowed : 16.67 % Favored : 80.69 % 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: 0.61 (0.27), residues: 1014 helix: 1.53 (0.24), residues: 504 sheet: -0.45 (0.52), residues: 97 loop : -0.77 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 854 HIS 0.002 0.000 HIS A 566 PHE 0.029 0.001 PHE A 759 TYR 0.025 0.001 TYR A 586 ARG 0.004 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 452 MET cc_start: 0.6942 (ptt) cc_final: 0.6461 (ptt) REVERT: A 573 GLU cc_start: 0.6883 (pt0) cc_final: 0.6398 (pt0) REVERT: A 575 MET cc_start: 0.6370 (mmt) cc_final: 0.6008 (mmm) REVERT: A 599 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7196 (pt) REVERT: A 758 GLN cc_start: 0.7629 (mt0) cc_final: 0.6787 (tp40) REVERT: A 784 GLU cc_start: 0.6211 (mm-30) cc_final: 0.5055 (mm-30) REVERT: A 1023 MET cc_start: 0.1699 (mmt) cc_final: 0.0611 (mtp) outliers start: 23 outliers final: 17 residues processed: 125 average time/residue: 0.1669 time to fit residues: 29.8107 Evaluate side-chains 122 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 980 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.175487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.139666 restraints weight = 8965.402| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.83 r_work: 0.3478 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8017 Z= 0.279 Angle : 0.856 32.141 10882 Z= 0.367 Chirality : 0.044 0.171 1276 Planarity : 0.005 0.051 1387 Dihedral : 4.232 16.128 1078 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.99 % Allowed : 16.90 % Favored : 80.11 % 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: 0.38 (0.27), residues: 1014 helix: 1.28 (0.24), residues: 504 sheet: -0.75 (0.51), residues: 99 loop : -0.72 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 36 HIS 0.003 0.001 HIS A 566 PHE 0.027 0.002 PHE A 759 TYR 0.035 0.002 TYR A 586 ARG 0.003 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.834 Fit side-chains REVERT: A 467 ARG cc_start: 0.6727 (tmt170) cc_final: 0.6102 (tpt90) REVERT: A 573 GLU cc_start: 0.6832 (pt0) cc_final: 0.6284 (pt0) REVERT: A 599 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7181 (pt) REVERT: A 715 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.7717 (tp) REVERT: A 784 GLU cc_start: 0.6209 (mm-30) cc_final: 0.5106 (mm-30) outliers start: 26 outliers final: 20 residues processed: 125 average time/residue: 0.1591 time to fit residues: 28.8613 Evaluate side-chains 126 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 980 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 48 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 5 optimal weight: 0.0570 chunk 100 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.179325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.144601 restraints weight = 8732.121| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.77 r_work: 0.3541 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8017 Z= 0.164 Angle : 0.817 29.870 10882 Z= 0.342 Chirality : 0.041 0.163 1276 Planarity : 0.005 0.050 1387 Dihedral : 3.944 15.094 1078 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.41 % Allowed : 17.47 % Favored : 80.11 % 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: 0.58 (0.27), residues: 1014 helix: 1.49 (0.24), residues: 504 sheet: -0.44 (0.52), residues: 99 loop : -0.76 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 854 HIS 0.002 0.001 HIS A 566 PHE 0.029 0.001 PHE A 759 TYR 0.031 0.001 TYR A 586 ARG 0.003 0.000 ARG A 549 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.814 Fit side-chains REVERT: A 536 MET cc_start: 0.7142 (tpt) cc_final: 0.6721 (tpt) REVERT: A 573 GLU cc_start: 0.6875 (pt0) cc_final: 0.6379 (pt0) REVERT: A 575 MET cc_start: 0.6422 (mmt) cc_final: 0.6085 (mmm) REVERT: A 599 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7171 (pt) REVERT: A 715 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.7853 (tp) REVERT: A 731 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7356 (mt-10) REVERT: A 758 GLN cc_start: 0.7668 (mt0) cc_final: 0.6783 (tp40) REVERT: A 784 GLU cc_start: 0.6224 (mm-30) cc_final: 0.5108 (mm-30) REVERT: A 1023 MET cc_start: 0.1451 (mmt) cc_final: 0.0482 (mtp) outliers start: 21 outliers final: 16 residues processed: 125 average time/residue: 0.1826 time to fit residues: 32.8697 Evaluate side-chains 126 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 980 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 6.9990 chunk 61 optimal weight: 0.0770 chunk 97 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 86 optimal weight: 0.0040 overall best weight: 0.5554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.180500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.145962 restraints weight = 8762.404| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.76 r_work: 0.3557 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8017 Z= 0.159 Angle : 0.814 29.629 10882 Z= 0.339 Chirality : 0.041 0.161 1276 Planarity : 0.004 0.050 1387 Dihedral : 3.849 15.697 1078 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.30 % Allowed : 17.93 % Favored : 79.77 % 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 (0.27), residues: 1014 helix: 1.57 (0.24), residues: 505 sheet: -0.31 (0.52), residues: 99 loop : -0.71 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 854 HIS 0.002 0.000 HIS A 566 PHE 0.028 0.001 PHE A 759 TYR 0.030 0.001 TYR A 586 ARG 0.003 0.000 ARG A 549 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4389.94 seconds wall clock time: 78 minutes 25.44 seconds (4705.44 seconds total)