Starting phenix.real_space_refine on Wed Jun 3 21:48:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pko_71702/06_2026/9pko_71702_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pko_71702/06_2026/9pko_71702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pko_71702/06_2026/9pko_71702_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pko_71702/06_2026/9pko_71702_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pko_71702/06_2026/9pko_71702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pko_71702/06_2026/9pko_71702.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 48 5.16 5 C 5790 2.51 5 N 1276 2.21 5 O 1386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8503 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3999 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 484} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 3999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3999 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 484} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 254 Unusual residues: {' K': 3, 'LMT': 29} Classifications: {'undetermined': 32} Link IDs: {None: 31} Unresolved non-hydrogen bonds: 822 Unresolved non-hydrogen angles: 1170 Unresolved non-hydrogen dihedrals: 1605 Unresolved non-hydrogen chiralities: 290 Chain: "B" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 251 Unusual residues: {'LMT': 29} Classifications: {'undetermined': 29} Link IDs: {None: 28} Unresolved non-hydrogen bonds: 822 Unresolved non-hydrogen angles: 1170 Unresolved non-hydrogen dihedrals: 1605 Unresolved non-hydrogen chiralities: 290 Time building chain proxies: 2.07, per 1000 atoms: 0.24 Number of scatterers: 8503 At special positions: 0 Unit cell: (91.797, 101.721, 124.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 48 16.00 O 1386 8.00 N 1276 7.00 C 5790 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 293.9 milliseconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 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 2 sheets defined 81.4% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 96 through 103 removed outlier: 3.509A pdb=" N ILE A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 121 Processing helix chain 'A' and resid 121 through 143 Proline residue: A 131 - end of helix removed outlier: 3.808A pdb=" N VAL A 139 " --> pdb=" O MET A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 184 Processing helix chain 'A' and resid 188 through 219 removed outlier: 3.603A pdb=" N ARG A 216 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU A 217 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 257 removed outlier: 3.557A pdb=" N TYR A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 Processing helix chain 'A' and resid 272 through 295 Processing helix chain 'A' and resid 299 through 312 Processing helix chain 'A' and resid 323 through 351 Processing helix chain 'A' and resid 356 through 380 Processing helix chain 'A' and resid 384 through 431 removed outlier: 3.892A pdb=" N GLY A 422 " --> pdb=" O PHE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 446 Processing helix chain 'A' and resid 457 through 500 removed outlier: 3.727A pdb=" N SER A 466 " --> pdb=" O VAL A 462 " (cutoff:3.500A) Proline residue: A 473 - end of helix removed outlier: 3.533A pdb=" N ASP A 492 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 651 removed outlier: 4.082A pdb=" N GLN A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 642 " --> pdb=" O LEU A 638 " (cutoff:3.500A) Proline residue: A 643 - end of helix Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'A' and resid 674 through 678 Processing helix chain 'A' and resid 681 through 706 removed outlier: 4.089A pdb=" N GLU A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE A 706 " --> pdb=" O VAL A 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 96 through 103 removed outlier: 3.510A pdb=" N ILE B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 121 Processing helix chain 'B' and resid 121 through 143 Proline residue: B 131 - end of helix removed outlier: 3.807A pdb=" N VAL B 139 " --> pdb=" O MET B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 184 Processing helix chain 'B' and resid 188 through 219 removed outlier: 3.603A pdb=" N ARG B 216 " --> pdb=" O PHE B 212 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU B 217 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE B 218 " --> pdb=" O THR B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 257 removed outlier: 3.558A pdb=" N TYR B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 272 Processing helix chain 'B' and resid 272 through 295 Processing helix chain 'B' and resid 299 through 312 Processing helix chain 'B' and resid 323 through 351 Processing helix chain 'B' and resid 356 through 380 Processing helix chain 'B' and resid 384 through 431 removed outlier: 3.892A pdb=" N GLY B 422 " --> pdb=" O PHE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 446 Processing helix chain 'B' and resid 457 through 500 removed outlier: 3.727A pdb=" N SER B 466 " --> pdb=" O VAL B 462 " (cutoff:3.500A) Proline residue: B 473 - end of helix removed outlier: 3.533A pdb=" N ASP B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 651 removed outlier: 4.082A pdb=" N GLN B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 642 " --> pdb=" O LEU B 638 " (cutoff:3.500A) Proline residue: B 643 - end of helix Processing helix chain 'B' and resid 657 through 662 Processing helix chain 'B' and resid 674 through 678 Processing helix chain 'B' and resid 681 through 706 removed outlier: 4.088A pdb=" N GLU B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE B 706 " --> pdb=" O VAL B 702 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 154 through 155 removed outlier: 4.608A pdb=" N LYS A 146 " --> pdb=" O VAL A 155 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 154 through 155 removed outlier: 4.608A pdb=" N LYS B 146 " --> pdb=" O VAL B 155 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1860 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2408 1.34 - 1.46: 1979 1.46 - 1.58: 4171 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 8642 Sorted by residual: bond pdb=" CA SER B 228 " pdb=" CB SER B 228 " ideal model delta sigma weight residual 1.530 1.467 0.063 1.52e-02 4.33e+03 1.71e+01 bond pdb=" CA SER A 228 " pdb=" CB SER A 228 " ideal model delta sigma weight residual 1.530 1.467 0.063 1.52e-02 4.33e+03 1.71e+01 bond pdb=" N PHE A 463 " pdb=" CA PHE A 463 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.18e-02 7.18e+03 7.06e+00 bond pdb=" N PHE B 463 " pdb=" CA PHE B 463 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.18e-02 7.18e+03 7.06e+00 bond pdb=" CA ALA B 413 " pdb=" CB ALA B 413 " ideal model delta sigma weight residual 1.530 1.492 0.038 1.58e-02 4.01e+03 5.87e+00 ... (remaining 8637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 11277 1.36 - 2.72: 157 2.72 - 4.08: 66 4.08 - 5.44: 14 5.44 - 6.80: 2 Bond angle restraints: 11516 Sorted by residual: angle pdb=" C PHE A 463 " pdb=" CA PHE A 463 " pdb=" CB PHE A 463 " ideal model delta sigma weight residual 110.95 104.15 6.80 1.55e+00 4.16e-01 1.92e+01 angle pdb=" C PHE B 463 " pdb=" CA PHE B 463 " pdb=" CB PHE B 463 " ideal model delta sigma weight residual 110.95 104.17 6.78 1.55e+00 4.16e-01 1.91e+01 angle pdb=" CA LEU B 410 " pdb=" C LEU B 410 " pdb=" O LEU B 410 " ideal model delta sigma weight residual 120.63 116.41 4.22 1.08e+00 8.57e-01 1.52e+01 angle pdb=" CA LEU A 410 " pdb=" C LEU A 410 " pdb=" O LEU A 410 " ideal model delta sigma weight residual 120.63 116.42 4.21 1.08e+00 8.57e-01 1.52e+01 angle pdb=" C SER A 407 " pdb=" N LEU A 408 " pdb=" CA LEU A 408 " ideal model delta sigma weight residual 120.65 115.73 4.92 1.32e+00 5.74e-01 1.39e+01 ... (remaining 11511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.97: 4786 11.97 - 23.95: 272 23.95 - 35.92: 90 35.92 - 47.90: 14 47.90 - 59.87: 8 Dihedral angle restraints: 5170 sinusoidal: 2216 harmonic: 2954 Sorted by residual: dihedral pdb=" CA LEU B 680 " pdb=" C LEU B 680 " pdb=" N LYS B 681 " pdb=" CA LYS B 681 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA LEU A 680 " pdb=" C LEU A 680 " pdb=" N LYS A 681 " pdb=" CA LYS A 681 " ideal model delta harmonic sigma weight residual 180.00 158.51 21.49 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CB MET A 181 " pdb=" CG MET A 181 " pdb=" SD MET A 181 " pdb=" CE MET A 181 " ideal model delta sinusoidal sigma weight residual 60.00 109.53 -49.53 3 1.50e+01 4.44e-03 8.79e+00 ... (remaining 5167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 956 0.042 - 0.085: 282 0.085 - 0.127: 48 0.127 - 0.170: 6 0.170 - 0.212: 2 Chirality restraints: 1294 Sorted by residual: chirality pdb=" CA ILE B 412 " pdb=" N ILE B 412 " pdb=" C ILE B 412 " pdb=" CB ILE B 412 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE A 412 " pdb=" N ILE A 412 " pdb=" C ILE A 412 " pdb=" CB ILE A 412 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA PHE B 463 " pdb=" N PHE B 463 " pdb=" C PHE B 463 " pdb=" CB PHE B 463 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.96e-01 ... (remaining 1291 not shown) Planarity restraints: 1350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 462 " -0.022 2.00e-02 2.50e+03 4.42e-02 1.96e+01 pdb=" C VAL A 462 " 0.077 2.00e-02 2.50e+03 pdb=" O VAL A 462 " -0.029 2.00e-02 2.50e+03 pdb=" N PHE A 463 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 462 " 0.022 2.00e-02 2.50e+03 4.41e-02 1.95e+01 pdb=" C VAL B 462 " -0.076 2.00e-02 2.50e+03 pdb=" O VAL B 462 " 0.029 2.00e-02 2.50e+03 pdb=" N PHE B 463 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 463 " 0.006 2.00e-02 2.50e+03 1.27e-02 1.60e+00 pdb=" C PHE B 463 " -0.022 2.00e-02 2.50e+03 pdb=" O PHE B 463 " 0.008 2.00e-02 2.50e+03 pdb=" N PHE B 464 " 0.007 2.00e-02 2.50e+03 ... (remaining 1347 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.88: 2953 2.88 - 3.44: 9985 3.44 - 4.01: 15144 4.01 - 4.57: 22696 4.57 - 5.14: 31482 Nonbonded interactions: 82260 Sorted by model distance: nonbonded pdb=" O LEU A 408 " pdb=" OG1 THR A 411 " model vdw 2.315 3.040 nonbonded pdb=" O LEU B 408 " pdb=" OG1 THR B 411 " model vdw 2.315 3.040 nonbonded pdb=" CG GLN A 427 " pdb=" O TRP A 432 " model vdw 2.494 3.440 nonbonded pdb=" CG GLN B 427 " pdb=" O TRP B 432 " model vdw 2.495 3.440 nonbonded pdb=" O PHE A 463 " pdb=" C PHE A 464 " model vdw 2.528 3.270 ... (remaining 82255 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 82 through 706 or (resid 904 and (name C1 or name C2 or na \ me C3 or name C4 or name C5 or name C6 )) or (resid 905 and (name C2 or name C3 \ or name C4 or name C5 or name C6 )) or (resid 906 and (name C4 or name C5 or nam \ e C6 )) or (resid 907 and (name C3 or name C4 or name C5 or name C6 )) or (resid \ 908 and (name C4 or name C5 or name C6 or name C7 or name C8 )) or resid 909 or \ (resid 910 and (name C3 or name C4 or name C5 or name C6 or name C7 or name C8 \ )) or resid 911 through 913 or (resid 914 and (name C10 or name C11 or name C12 \ or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or \ name C9 )) or (resid 915 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 )) or (resid 916 and (name C3 or name C4 or name C5 or n \ ame C6 or name C7 or name C8 )) or (resid 917 and (name C2 or name C3 or name C4 \ or name C5 or name C6 or name C7 )) or resid 918 or (resid 919 and (name C4 or \ name C5 or name C6 or name C7 or name C8 or name C9 )) or (resid 920 and (name C \ 10 or name C11 or name C12 or name C2 or name C3 or name C4 or name C5 or name C \ 6 or name C7 or name C8 or name C9 )) or resid 921 or (resid 922 and (name C2 or \ name C3 or name C4 or name C5 or name C6 or name C7 or name C8 )) or (resid 923 \ and (name C5 or name C6 or name C7 or name C8 or name C9 )) or (resid 924 throu \ gh 925 and (name C5 or name C6 or name C7 or name C8 )) or (resid 926 and (name \ C5 or name C6 or name C7 )) or resid 927 through 928 or (resid 929 and (name C5 \ or name C6 or name C7 or name C8 )))) selection = (chain 'B' and (resid 82 through 706 or resid 804 through 805 or (resid 806 and \ (name C4 or name C5 or name C6 )) or (resid 807 and (name C3 or name C4 or name \ C5 or name C6 )) or (resid 808 and (name C4 or name C5 or name C6 or name C7 or \ name C8 )) or (resid 809 and (name C10 or name C11 or name C3 or name C4 or name \ C5 or name C6 or name C7 or name C8 or name C9 )) or (resid 810 and (name C3 or \ name C4 or name C5 or name C6 or name C7 or name C8 )) or (resid 811 through 81 \ 2 and (name C10 or name C11 or name C12 or name C3 or name C4 or name C5 or name \ C6 or name C7 or name C8 or name C9 )) or resid 813 through 816 or (resid 817 a \ nd (name C2 or name C3 or name C4 or name C5 or name C6 or name C7 )) or (resid \ 818 and (name C3 or name C4 or name C5 or name C6 or name C7 or name C8 )) or re \ sid 819 through 820 or (resid 821 and (name C4 or name C5 or name C6 or name C7 \ or name C8 or name C9 )) or (resid 822 and (name C2 or name C3 or name C4 or nam \ e C5 or name C6 or name C7 or name C8 )) or resid 823 or (resid 824 through 825 \ and (name C5 or name C6 or name C7 or name C8 )) or (resid 826 and (name C5 or n \ ame C6 or name C7 )) or (resid 827 and (name C3 or name C4 or name C5 or name C6 \ or name C7 or name C8 )) or resid 828 or (resid 829 and (name C5 or name C6 or \ name C7 or name C8 )))) } 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: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.920 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 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 0.063 8642 Z= 0.192 Angle : 0.481 6.798 11516 Z= 0.302 Chirality : 0.039 0.212 1294 Planarity : 0.004 0.044 1350 Dihedral : 8.714 59.869 3262 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.27), residues: 1002 helix: 2.08 (0.18), residues: 778 sheet: None (None), residues: 0 loop : 0.70 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 699 TYR 0.006 0.001 TYR B 260 PHE 0.009 0.001 PHE B 463 TRP 0.005 0.001 TRP A 115 HIS 0.001 0.000 HIS B 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.19 ( 8642) covalent geometry : angle 0.48144 / 0.30 (11516) hydrogen bonds : bond 0.19701 / 13.29 ( 624) hydrogen bonds : angle 5.68780 / 4.13 ( 1860) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 83 MET cc_start: 0.5947 (mmm) cc_final: 0.5671 (mmm) REVERT: A 96 ARG cc_start: 0.8243 (mtp-110) cc_final: 0.7949 (mtp-110) REVERT: A 392 MET cc_start: 0.9052 (tpt) cc_final: 0.8838 (tpt) REVERT: A 488 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8874 (mm-30) REVERT: B 83 MET cc_start: 0.6033 (mmm) cc_final: 0.5744 (mmm) REVERT: B 392 MET cc_start: 0.9038 (tpt) cc_final: 0.8831 (tpt) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.7490 time to fit residues: 72.4178 Evaluate side-chains 62 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 268 GLN B 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.077625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.061204 restraints weight = 21021.525| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.90 r_work: 0.2766 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8642 Z= 0.161 Angle : 0.493 8.585 11516 Z= 0.258 Chirality : 0.039 0.146 1294 Planarity : 0.004 0.033 1350 Dihedral : 6.367 56.935 1410 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.71 % Allowed : 5.13 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.84 (0.26), residues: 1002 helix: 3.08 (0.18), residues: 772 sheet: None (None), residues: 0 loop : 0.57 (0.43), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.014 0.001 TYR B 439 PHE 0.006 0.001 PHE B 464 TRP 0.007 0.001 TRP A 115 HIS 0.002 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 8642) covalent geometry : angle 0.49325 / 0.26 (11516) hydrogen bonds : bond 0.05415 / 3.69 ( 624) hydrogen bonds : angle 3.84430 / 2.82 ( 1860) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.347 Fit side-chains REVERT: A 83 MET cc_start: 0.6231 (mmm) cc_final: 0.6011 (mmm) REVERT: A 392 MET cc_start: 0.9189 (tpt) cc_final: 0.8912 (tpt) REVERT: A 488 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8797 (mp0) REVERT: B 83 MET cc_start: 0.6274 (mmm) cc_final: 0.6058 (mmm) REVERT: B 392 MET cc_start: 0.9171 (tpt) cc_final: 0.8895 (tpt) REVERT: B 488 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8819 (mp0) outliers start: 15 outliers final: 2 residues processed: 69 average time/residue: 0.6280 time to fit residues: 46.1092 Evaluate side-chains 56 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain B residue 638 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 51 optimal weight: 0.0980 chunk 88 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.078960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.062938 restraints weight = 21032.185| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.80 r_work: 0.2818 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8642 Z= 0.104 Angle : 0.438 5.372 11516 Z= 0.224 Chirality : 0.038 0.143 1294 Planarity : 0.003 0.032 1350 Dihedral : 6.107 55.804 1410 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.14 % Allowed : 7.63 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.28 (0.26), residues: 1002 helix: 3.42 (0.18), residues: 772 sheet: None (None), residues: 0 loop : 0.65 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 699 TYR 0.016 0.001 TYR A 439 PHE 0.006 0.001 PHE A 440 TRP 0.005 0.001 TRP B 115 HIS 0.001 0.000 HIS A 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 8642) covalent geometry : angle 0.43818 / 0.22 (11516) hydrogen bonds : bond 0.03979 / 2.72 ( 624) hydrogen bonds : angle 3.48905 / 2.56 ( 1860) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.302 Fit side-chains REVERT: A 392 MET cc_start: 0.9176 (tpt) cc_final: 0.8887 (tpt) REVERT: A 488 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8764 (mp0) REVERT: A 496 TRP cc_start: 0.7632 (t-100) cc_final: 0.7067 (t-100) REVERT: A 704 MET cc_start: 0.9105 (ttm) cc_final: 0.8441 (tmm) REVERT: B 488 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8777 (mp0) REVERT: B 496 TRP cc_start: 0.7639 (t-100) cc_final: 0.7090 (t-100) REVERT: B 704 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8467 (tmm) outliers start: 10 outliers final: 3 residues processed: 65 average time/residue: 0.5980 time to fit residues: 41.4841 Evaluate side-chains 58 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 704 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 17 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.075829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.060670 restraints weight = 21211.170| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.76 r_work: 0.2765 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8642 Z= 0.130 Angle : 0.455 5.665 11516 Z= 0.232 Chirality : 0.038 0.146 1294 Planarity : 0.003 0.030 1350 Dihedral : 6.300 55.808 1410 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.59 % Allowed : 7.86 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.28 (0.26), residues: 1002 helix: 3.45 (0.18), residues: 768 sheet: None (None), residues: 0 loop : 0.59 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 699 TYR 0.016 0.001 TYR A 439 PHE 0.005 0.001 PHE B 464 TRP 0.005 0.001 TRP A 115 HIS 0.003 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 8642) covalent geometry : angle 0.45485 / 0.23 (11516) hydrogen bonds : bond 0.03893 / 2.65 ( 624) hydrogen bonds : angle 3.45377 / 2.53 ( 1860) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.349 Fit side-chains REVERT: A 496 TRP cc_start: 0.7685 (t-100) cc_final: 0.7069 (t-100) REVERT: A 704 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8456 (tmm) REVERT: B 496 TRP cc_start: 0.7662 (t-100) cc_final: 0.6997 (t-100) REVERT: B 704 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8499 (tmm) outliers start: 14 outliers final: 2 residues processed: 66 average time/residue: 0.5862 time to fit residues: 41.4887 Evaluate side-chains 56 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 704 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 4.9990 chunk 67 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 660 GLN B 134 ASN B 660 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.076890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.061653 restraints weight = 20919.527| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.75 r_work: 0.2809 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8642 Z= 0.105 Angle : 0.446 6.891 11516 Z= 0.227 Chirality : 0.038 0.146 1294 Planarity : 0.003 0.031 1350 Dihedral : 6.128 56.980 1410 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.25 % Allowed : 9.57 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.37 (0.26), residues: 1002 helix: 3.52 (0.18), residues: 768 sheet: None (None), residues: 0 loop : 0.60 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 402 TYR 0.015 0.001 TYR A 439 PHE 0.005 0.001 PHE A 440 TRP 0.004 0.000 TRP A 661 HIS 0.002 0.000 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 8642) covalent geometry : angle 0.44644 / 0.23 (11516) hydrogen bonds : bond 0.03558 / 2.43 ( 624) hydrogen bonds : angle 3.37356 / 2.47 ( 1860) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.302 Fit side-chains REVERT: A 496 TRP cc_start: 0.7693 (t-100) cc_final: 0.7054 (t-100) REVERT: A 704 MET cc_start: 0.9081 (ttm) cc_final: 0.8513 (tmm) REVERT: B 496 TRP cc_start: 0.7673 (t-100) cc_final: 0.7019 (t-100) REVERT: B 704 MET cc_start: 0.9064 (ttm) cc_final: 0.8493 (tmm) outliers start: 11 outliers final: 2 residues processed: 63 average time/residue: 0.5207 time to fit residues: 35.3816 Evaluate side-chains 54 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain B residue 412 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.075518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.060096 restraints weight = 20837.098| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.77 r_work: 0.2735 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8642 Z= 0.115 Angle : 0.439 6.084 11516 Z= 0.223 Chirality : 0.038 0.146 1294 Planarity : 0.003 0.031 1350 Dihedral : 6.143 57.699 1410 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.03 % Allowed : 9.11 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.36 (0.26), residues: 1002 helix: 3.51 (0.18), residues: 768 sheet: None (None), residues: 0 loop : 0.58 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 216 TYR 0.015 0.001 TYR A 439 PHE 0.005 0.001 PHE A 463 TRP 0.004 0.001 TRP B 661 HIS 0.002 0.000 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 8642) covalent geometry : angle 0.43890 / 0.22 (11516) hydrogen bonds : bond 0.03564 / 2.43 ( 624) hydrogen bonds : angle 3.36549 / 2.47 ( 1860) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.268 Fit side-chains REVERT: A 496 TRP cc_start: 0.7706 (t-100) cc_final: 0.7034 (t-100) REVERT: A 696 MET cc_start: 0.8832 (mtt) cc_final: 0.8585 (tpp) REVERT: A 697 MET cc_start: 0.7833 (mtt) cc_final: 0.7596 (mtm) REVERT: A 704 MET cc_start: 0.9118 (ttm) cc_final: 0.8551 (tmm) REVERT: B 633 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8656 (tmm) REVERT: B 704 MET cc_start: 0.9120 (ttm) cc_final: 0.8558 (tmm) outliers start: 9 outliers final: 5 residues processed: 61 average time/residue: 0.5351 time to fit residues: 35.2191 Evaluate side-chains 58 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 638 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 chunk 59 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.075785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.060373 restraints weight = 21074.956| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.79 r_work: 0.2740 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8642 Z= 0.104 Angle : 0.426 5.768 11516 Z= 0.217 Chirality : 0.037 0.145 1294 Planarity : 0.003 0.031 1350 Dihedral : 6.056 58.775 1410 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.23 % Allowed : 10.25 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.40 (0.26), residues: 1002 helix: 3.54 (0.18), residues: 768 sheet: None (None), residues: 0 loop : 0.59 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 269 TYR 0.015 0.001 TYR A 439 PHE 0.005 0.001 PHE A 440 TRP 0.004 0.000 TRP A 661 HIS 0.002 0.000 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 ( 8642) covalent geometry : angle 0.42586 / 0.22 (11516) hydrogen bonds : bond 0.03451 / 2.36 ( 624) hydrogen bonds : angle 3.34208 / 2.45 ( 1860) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.347 Fit side-chains REVERT: A 696 MET cc_start: 0.8830 (mtt) cc_final: 0.8582 (tpp) REVERT: A 697 MET cc_start: 0.7834 (mtt) cc_final: 0.7522 (mtm) REVERT: A 704 MET cc_start: 0.9108 (ttm) cc_final: 0.8549 (tmm) REVERT: B 496 TRP cc_start: 0.7682 (t-100) cc_final: 0.7057 (t60) REVERT: B 704 MET cc_start: 0.9129 (ttm) cc_final: 0.8567 (tmm) outliers start: 2 outliers final: 2 residues processed: 58 average time/residue: 0.6409 time to fit residues: 39.8353 Evaluate side-chains 54 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain B residue 412 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.073702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.058392 restraints weight = 21065.849| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.75 r_work: 0.2689 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8642 Z= 0.161 Angle : 0.474 7.240 11516 Z= 0.241 Chirality : 0.039 0.147 1294 Planarity : 0.003 0.031 1350 Dihedral : 6.613 58.888 1410 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.68 % Allowed : 9.68 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.18 (0.26), residues: 1002 helix: 3.38 (0.18), residues: 780 sheet: None (None), residues: 0 loop : 0.35 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 216 TYR 0.015 0.001 TYR B 439 PHE 0.007 0.001 PHE B 112 TRP 0.005 0.001 TRP B 661 HIS 0.003 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 8642) covalent geometry : angle 0.47407 / 0.24 (11516) hydrogen bonds : bond 0.03955 / 2.70 ( 624) hydrogen bonds : angle 3.45572 / 2.53 ( 1860) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.343 Fit side-chains REVERT: A 696 MET cc_start: 0.8860 (mtt) cc_final: 0.8636 (tpp) REVERT: A 697 MET cc_start: 0.7870 (mtt) cc_final: 0.7477 (mtm) REVERT: A 704 MET cc_start: 0.9149 (ttm) cc_final: 0.8623 (tmm) REVERT: B 697 MET cc_start: 0.7851 (mtt) cc_final: 0.7492 (mtm) REVERT: B 704 MET cc_start: 0.9140 (ttm) cc_final: 0.8596 (tmm) outliers start: 6 outliers final: 3 residues processed: 58 average time/residue: 0.5906 time to fit residues: 36.8235 Evaluate side-chains 53 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 686 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.073650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.058231 restraints weight = 20986.751| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.76 r_work: 0.2670 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8642 Z= 0.179 Angle : 0.484 7.257 11516 Z= 0.247 Chirality : 0.040 0.146 1294 Planarity : 0.003 0.032 1350 Dihedral : 6.974 59.870 1410 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.68 % Allowed : 9.57 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.10 (0.26), residues: 1002 helix: 3.34 (0.18), residues: 768 sheet: None (None), residues: 0 loop : 0.45 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 677 TYR 0.016 0.001 TYR B 439 PHE 0.007 0.001 PHE B 464 TRP 0.005 0.001 TRP B 115 HIS 0.003 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 ( 8642) covalent geometry : angle 0.48395 / 0.25 (11516) hydrogen bonds : bond 0.04039 / 2.75 ( 624) hydrogen bonds : angle 3.49417 / 2.56 ( 1860) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.324 Fit side-chains REVERT: A 496 TRP cc_start: 0.7689 (t-100) cc_final: 0.7351 (t60) REVERT: A 696 MET cc_start: 0.8892 (mtt) cc_final: 0.8682 (tpp) REVERT: A 697 MET cc_start: 0.7863 (mtt) cc_final: 0.7486 (mtm) REVERT: A 704 MET cc_start: 0.9172 (ttm) cc_final: 0.8674 (tmm) REVERT: B 496 TRP cc_start: 0.7694 (t-100) cc_final: 0.7364 (t60) REVERT: B 633 MET cc_start: 0.8899 (ppp) cc_final: 0.8549 (ppp) REVERT: B 697 MET cc_start: 0.7928 (mtt) cc_final: 0.7588 (mtm) REVERT: B 704 MET cc_start: 0.9159 (ttm) cc_final: 0.8639 (tmm) outliers start: 6 outliers final: 5 residues processed: 59 average time/residue: 0.5682 time to fit residues: 36.0401 Evaluate side-chains 56 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 686 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 0.0670 chunk 41 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.075272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.059919 restraints weight = 20884.788| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.77 r_work: 0.2721 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8642 Z= 0.104 Angle : 0.444 7.348 11516 Z= 0.227 Chirality : 0.038 0.145 1294 Planarity : 0.003 0.034 1350 Dihedral : 6.394 56.782 1410 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.23 % Allowed : 10.48 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.20 (0.26), residues: 1002 helix: 3.40 (0.18), residues: 768 sheet: None (None), residues: 0 loop : 0.54 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 269 TYR 0.015 0.001 TYR A 439 PHE 0.005 0.001 PHE B 463 TRP 0.004 0.000 TRP B 661 HIS 0.002 0.000 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 8642) covalent geometry : angle 0.44437 / 0.23 (11516) hydrogen bonds : bond 0.03575 / 2.44 ( 624) hydrogen bonds : angle 3.40873 / 2.50 ( 1860) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.336 Fit side-chains REVERT: A 496 TRP cc_start: 0.7651 (t-100) cc_final: 0.7327 (t60) REVERT: A 697 MET cc_start: 0.7757 (mtt) cc_final: 0.7405 (mtm) REVERT: A 704 MET cc_start: 0.9136 (ttm) cc_final: 0.8689 (tmm) REVERT: B 496 TRP cc_start: 0.7687 (t-100) cc_final: 0.7360 (t60) REVERT: B 697 MET cc_start: 0.7799 (mtt) cc_final: 0.7386 (mtm) REVERT: B 704 MET cc_start: 0.9128 (ttm) cc_final: 0.8678 (tmm) outliers start: 2 outliers final: 2 residues processed: 57 average time/residue: 0.5758 time to fit residues: 35.2160 Evaluate side-chains 55 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain B residue 412 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 95 optimal weight: 0.2980 chunk 48 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.075414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.060017 restraints weight = 20898.784| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.77 r_work: 0.2729 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8642 Z= 0.106 Angle : 0.450 7.241 11516 Z= 0.229 Chirality : 0.038 0.146 1294 Planarity : 0.003 0.034 1350 Dihedral : 6.172 54.170 1410 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.22 (0.26), residues: 1002 helix: 3.42 (0.18), residues: 768 sheet: None (None), residues: 0 loop : 0.55 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 269 TYR 0.014 0.001 TYR A 439 PHE 0.005 0.001 PHE B 218 TRP 0.004 0.000 TRP B 661 HIS 0.002 0.000 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 8642) covalent geometry : angle 0.45041 / 0.23 (11516) hydrogen bonds : bond 0.03513 / 2.38 ( 624) hydrogen bonds : angle 3.38194 / 2.48 ( 1860) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2212.22 seconds wall clock time: 38 minutes 41.76 seconds (2321.76 seconds total)