Starting phenix.real_space_refine on Fri Jul 3 03:19:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gy0_51680/07_2026/9gy0_51680.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gy0_51680/07_2026/9gy0_51680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gy0_51680/07_2026/9gy0_51680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gy0_51680/07_2026/9gy0_51680.map" model { file = "/net/cci-nas-00/data/ceres_data/9gy0_51680/07_2026/9gy0_51680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gy0_51680/07_2026/9gy0_51680.cif" } resolution = 3.42 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= -0.001 sd= 0.058 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 64 5.49 5 S 72 5.16 5 C 7297 2.51 5 N 2042 2.21 5 O 2390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11866 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4816 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 21, 'TRANS': 574} Chain breaks: 3 Chain: "B" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 605 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "C" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 471 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "D" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 251 Classifications: {'DNA': 12} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 11} Chain: "E" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1964 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1812 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 7, 'TRANS': 227} Chain breaks: 3 Chain: "G" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1946 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 7, 'TRANS': 245} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P DG B 21 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG B 21 " occ=0.00 Time building chain proxies: 2.39, per 1000 atoms: 0.20 Number of scatterers: 11866 At special positions: 0 Unit cell: (105.133, 104.219, 144.444, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 72 16.00 P 64 15.00 O 2390 8.00 N 2042 7.00 C 7297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 162 " distance=2.04 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: 0.64 Conformation dependent library (CDL) restraints added in 338.5 milliseconds 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 14 sheets defined 40.9% alpha, 19.8% beta 27 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 373 through 389 Processing helix chain 'A' and resid 389 through 394 removed outlier: 3.512A pdb=" N LEU A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 409 Processing helix chain 'A' and resid 411 through 424 removed outlier: 3.755A pdb=" N ARG A 424 " --> pdb=" O ARG A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 454 Processing helix chain 'A' and resid 458 through 462 Processing helix chain 'A' and resid 464 through 472 removed outlier: 3.678A pdb=" N GLU A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 484 Processing helix chain 'A' and resid 492 through 506 removed outlier: 3.932A pdb=" N GLN A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 532 removed outlier: 3.546A pdb=" N VAL A 522 " --> pdb=" O GLY A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 555 removed outlier: 4.552A pdb=" N THR A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 Processing helix chain 'A' and resid 598 through 622 Processing helix chain 'A' and resid 623 through 642 Processing helix chain 'A' and resid 646 through 651 removed outlier: 3.592A pdb=" N HIS A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 661 through 681 Processing helix chain 'A' and resid 682 through 695 removed outlier: 3.533A pdb=" N SER A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 717 Processing helix chain 'A' and resid 722 through 735 Processing helix chain 'A' and resid 740 through 755 removed outlier: 3.865A pdb=" N LEU A 746 " --> pdb=" O HIS A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 Processing helix chain 'A' and resid 813 through 825 Processing helix chain 'A' and resid 834 through 851 removed outlier: 4.063A pdb=" N PHE A 838 " --> pdb=" O GLU A 834 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ASP A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 879 removed outlier: 3.801A pdb=" N ARG A 879 " --> pdb=" O PHE A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 892 removed outlier: 3.678A pdb=" N ASP A 892 " --> pdb=" O GLN A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 909 Processing helix chain 'A' and resid 924 through 949 removed outlier: 6.172A pdb=" N GLY A 937 " --> pdb=" O SER A 933 " (cutoff:3.500A) Proline residue: A 938 - end of helix Processing helix chain 'A' and resid 950 through 955 Processing helix chain 'A' and resid 984 through 997 Processing helix chain 'E' and resid 9 through 23 removed outlier: 3.564A pdb=" N LYS E 20 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ASP E 21 " --> pdb=" O GLU E 17 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 80 Processing helix chain 'E' and resid 141 through 153 Processing helix chain 'E' and resid 209 through 216 Processing helix chain 'E' and resid 217 through 222 Proline residue: E 220 - end of helix No H-bonds generated for 'chain 'E' and resid 217 through 222' Processing helix chain 'F' and resid 8 through 19 removed outlier: 3.837A pdb=" N LEU F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 141 through 155 Processing helix chain 'F' and resid 209 through 215 Processing helix chain 'G' and resid 9 through 19 removed outlier: 3.570A pdb=" N LYS G 13 " --> pdb=" O GLY G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 57 Processing helix chain 'G' and resid 71 through 80 Processing helix chain 'G' and resid 94 through 96 No H-bonds generated for 'chain 'G' and resid 94 through 96' Processing helix chain 'G' and resid 141 through 155 Processing helix chain 'G' and resid 209 through 217 Processing helix chain 'G' and resid 218 through 222 Processing sheet with id=AA1, first strand: chain 'A' and resid 429 through 430 Processing sheet with id=AA2, first strand: chain 'A' and resid 778 through 783 removed outlier: 4.156A pdb=" N LYS A 778 " --> pdb=" O VAL A1001 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS A 970 " --> pdb=" O ASN A 965 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 963 " --> pdb=" O LYS A 972 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 58 through 62 removed outlier: 5.496A pdb=" N THR E 59 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG E 5 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG E 61 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN G 177 " --> pdb=" O GLU E 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AA5, first strand: chain 'E' and resid 34 through 36 Processing sheet with id=AA6, first strand: chain 'E' and resid 34 through 36 removed outlier: 4.430A pdb=" N LYS E 240 " --> pdb=" O THR E 224 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR E 224 " --> pdb=" O LYS E 240 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N MET E 229 " --> pdb=" O CYS E 135 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N CYS E 135 " --> pdb=" O MET E 229 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 204 through 208 removed outlier: 5.747A pdb=" N ALA E 157 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N SER E 172 " --> pdb=" O ALA E 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 25 through 27 removed outlier: 3.540A pdb=" N ALA F 26 " --> pdb=" O VAL F 70 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 29 through 30 Processing sheet with id=AB1, first strand: chain 'F' and resid 196 through 197 removed outlier: 3.563A pdb=" N THR F 196 " --> pdb=" O LYS F 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 177 through 181 removed outlier: 3.704A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 2 through 6 removed outlier: 3.930A pdb=" N PHE G 2 " --> pdb=" O ALA G 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 35 through 40 removed outlier: 4.580A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 157 through 159 552 hydrogen bonds defined for protein. 1572 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2023 1.32 - 1.45: 3279 1.45 - 1.57: 6662 1.57 - 1.69: 126 1.69 - 1.81: 111 Bond restraints: 12201 Sorted by residual: bond pdb=" C MET F 68 " pdb=" N GLY F 69 " ideal model delta sigma weight residual 1.331 1.409 -0.079 1.46e-02 4.69e+03 2.90e+01 bond pdb=" C ALA F 67 " pdb=" N MET F 68 " ideal model delta sigma weight residual 1.333 1.262 0.070 1.42e-02 4.96e+03 2.46e+01 bond pdb=" CA SER A 825 " pdb=" CB SER A 825 " ideal model delta sigma weight residual 1.531 1.463 0.068 1.69e-02 3.50e+03 1.60e+01 bond pdb=" C VAL G 236 " pdb=" N VAL G 237 " ideal model delta sigma weight residual 1.331 1.285 0.046 1.27e-02 6.20e+03 1.29e+01 bond pdb=" C3' DC B 25 " pdb=" C2' DC B 25 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 ... (remaining 12196 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 16145 1.64 - 3.27: 524 3.27 - 4.91: 76 4.91 - 6.55: 16 6.55 - 8.19: 6 Bond angle restraints: 16767 Sorted by residual: angle pdb=" C ALA G 67 " pdb=" N MET G 68 " pdb=" CA MET G 68 " ideal model delta sigma weight residual 122.36 114.17 8.19 1.42e+00 4.96e-01 3.32e+01 angle pdb=" N3 DT B 29 " pdb=" C4 DT B 29 " pdb=" O4 DT B 29 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT C 17 " pdb=" C4 DT C 17 " pdb=" O4 DT C 17 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N LEU A 713 " pdb=" CA LEU A 713 " pdb=" C LEU A 713 " ideal model delta sigma weight residual 111.69 106.58 5.11 1.23e+00 6.61e-01 1.73e+01 angle pdb=" N3 DT B 26 " pdb=" C4 DT B 26 " pdb=" O4 DT B 26 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 ... (remaining 16762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 5862 17.64 - 35.28: 858 35.28 - 52.93: 394 52.93 - 70.57: 92 70.57 - 88.21: 11 Dihedral angle restraints: 7217 sinusoidal: 3310 harmonic: 3907 Sorted by residual: dihedral pdb=" CB CYS G 135 " pdb=" SG CYS G 135 " pdb=" SG CYS G 162 " pdb=" CB CYS G 162 " ideal model delta sinusoidal sigma weight residual 93.00 45.21 47.79 1 1.00e+01 1.00e-02 3.15e+01 dihedral pdb=" CA HIS A 681 " pdb=" C HIS A 681 " pdb=" N MET A 682 " pdb=" CA MET A 682 " ideal model delta harmonic sigma weight residual 180.00 156.58 23.42 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" C LEU G 118 " pdb=" N LEU G 118 " pdb=" CA LEU G 118 " pdb=" CB LEU G 118 " ideal model delta harmonic sigma weight residual -122.60 -112.86 -9.74 0 2.50e+00 1.60e-01 1.52e+01 ... (remaining 7214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1868 0.106 - 0.213: 58 0.213 - 0.319: 2 0.319 - 0.425: 0 0.425 - 0.531: 3 Chirality restraints: 1931 Sorted by residual: chirality pdb=" P DT C 22 " pdb=" OP1 DT C 22 " pdb=" OP2 DT C 22 " pdb=" O5' DT C 22 " both_signs ideal model delta sigma weight residual True 2.34 -2.87 -0.53 2.00e-01 2.50e+01 7.06e+00 chirality pdb=" P DT C 21 " pdb=" OP1 DT C 21 " pdb=" OP2 DT C 21 " pdb=" O5' DT C 21 " both_signs ideal model delta sigma weight residual True 2.34 -2.86 -0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" CA LEU G 118 " pdb=" N LEU G 118 " pdb=" C LEU G 118 " pdb=" CB LEU G 118 " both_signs ideal model delta sigma weight residual False 2.51 2.94 -0.43 2.00e-01 2.50e+01 4.65e+00 ... (remaining 1928 not shown) Planarity restraints: 1913 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 706 " 0.218 9.50e-02 1.11e+02 9.80e-02 5.91e+00 pdb=" NE ARG A 706 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 706 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 706 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 706 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR G 114 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C TYR G 114 " 0.039 2.00e-02 2.50e+03 pdb=" O TYR G 114 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU G 115 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 704 " -0.169 9.50e-02 1.11e+02 7.57e-02 3.52e+00 pdb=" NE ARG A 704 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 704 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 704 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 704 " -0.006 2.00e-02 2.50e+03 ... (remaining 1910 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 348 2.70 - 3.25: 11421 3.25 - 3.80: 19621 3.80 - 4.35: 24494 4.35 - 4.90: 39917 Nonbonded interactions: 95801 Sorted by model distance: nonbonded pdb=" O2 DC B 36 " pdb=" N2 DG C 5 " model vdw 2.148 2.496 nonbonded pdb=" OG SER G 46 " pdb=" O TYR G 250 " model vdw 2.203 3.040 nonbonded pdb=" NE2 HIS A 718 " pdb=" OP1 DC B 17 " model vdw 2.248 3.120 nonbonded pdb=" OG SER G 222 " pdb=" O THR G 224 " model vdw 2.249 3.040 nonbonded pdb=" O PHE A 396 " pdb=" NZ LYS A 401 " model vdw 2.251 3.120 ... (remaining 95796 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 'E' and (resid 1 through 119 or resid 128 through 162 or resid 167 throug \ h 185 or resid 193 through 253)) selection = (chain 'F' and resid 1 through 253) selection = (chain 'G' and (resid 1 through 119 or resid 128 through 162 or resid 167 throug \ h 185 or resid 193 through 253)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.840 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.290 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 : 0.004 0.079 12202 Z= 0.312 Angle : 0.670 8.187 16769 Z= 0.453 Chirality : 0.049 0.531 1931 Planarity : 0.004 0.098 1913 Dihedral : 19.963 88.211 4670 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.21 % Allowed : 28.09 % Favored : 69.70 % 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: 0.20 (0.24), residues: 1319 helix: 1.32 (0.25), residues: 481 sheet: 0.15 (0.28), residues: 341 loop : -1.00 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 149 TYR 0.009 0.001 TYR A 418 PHE 0.024 0.001 PHE F 144 TRP 0.016 0.001 TRP A 708 HIS 0.007 0.001 HIS A 970 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.31 (12201) covalent geometry : angle 0.67038 / 0.45 (16767) SS BOND : bond 0.00590 / 0.37 ( 1) SS BOND : angle 0.88712 / 0.38 ( 2) hydrogen bonds : bond 0.13478 / 8.47 ( 622) hydrogen bonds : angle 5.60268 / 3.82 ( 1712) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 ARG cc_start: 0.7973 (mtm110) cc_final: 0.7720 (mtm110) REVERT: A 648 ARG cc_start: 0.7539 (mpt180) cc_final: 0.6777 (mmt180) REVERT: A 670 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7723 (mp) REVERT: A 764 HIS cc_start: 0.7376 (OUTLIER) cc_final: 0.6981 (m170) REVERT: A 950 ASP cc_start: 0.8229 (t70) cc_final: 0.7810 (t70) REVERT: E 116 MET cc_start: 0.7687 (mtp) cc_final: 0.7391 (mtp) REVERT: E 151 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7160 (mp) REVERT: E 240 LYS cc_start: 0.8173 (mttt) cc_final: 0.7620 (mmtm) REVERT: F 1 MET cc_start: 0.7663 (ppp) cc_final: 0.7311 (tmm) REVERT: F 30 ILE cc_start: 0.6765 (tp) cc_final: 0.6401 (mm) REVERT: F 49 GLN cc_start: 0.6182 (tp40) cc_final: 0.4782 (tm-30) REVERT: F 146 ARG cc_start: 0.8058 (mtt-85) cc_final: 0.7714 (mmm160) REVERT: F 168 LYS cc_start: 0.8279 (mttt) cc_final: 0.7940 (mptt) REVERT: F 199 MET cc_start: 0.5196 (ptp) cc_final: 0.4943 (mmm) REVERT: F 215 PHE cc_start: 0.6758 (m-10) cc_final: 0.6000 (m-80) REVERT: F 248 LYS cc_start: 0.5975 (mttt) cc_final: 0.5053 (tttm) REVERT: G 151 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7171 (mm) REVERT: G 229 MET cc_start: 0.4954 (mpp) cc_final: 0.4176 (mpp) outliers start: 26 outliers final: 19 residues processed: 173 average time/residue: 0.1124 time to fit residues: 26.9296 Evaluate side-chains 162 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 759 CYS Chi-restraints excluded: chain A residue 764 HIS Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 151 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.0470 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 861 ASN ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS G 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.182154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.142494 restraints weight = 18559.307| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 3.48 r_work: 0.3443 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.0686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12202 Z= 0.135 Angle : 0.553 8.607 16769 Z= 0.297 Chirality : 0.041 0.179 1931 Planarity : 0.004 0.037 1913 Dihedral : 18.902 70.621 2143 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.00 % Allowed : 25.87 % Favored : 70.13 % 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: 0.37 (0.24), residues: 1319 helix: 1.57 (0.24), residues: 492 sheet: 0.18 (0.28), residues: 333 loop : -1.04 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 149 TYR 0.017 0.002 TYR E 211 PHE 0.014 0.001 PHE F 144 TRP 0.009 0.001 TRP A 707 HIS 0.005 0.001 HIS E 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (12201) covalent geometry : angle 0.55242 / 0.30 (16767) SS BOND : bond 0.00493 / 0.31 ( 1) SS BOND : angle 1.08751 / 0.51 ( 2) hydrogen bonds : bond 0.04634 / 3.00 ( 622) hydrogen bonds : angle 4.74685 / 3.32 ( 1712) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7922 (mtmm) REVERT: A 498 ASP cc_start: 0.8724 (m-30) cc_final: 0.8359 (m-30) REVERT: A 648 ARG cc_start: 0.7552 (mpt180) cc_final: 0.6931 (mmt180) REVERT: A 765 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6770 (tp) REVERT: A 869 ASP cc_start: 0.8675 (m-30) cc_final: 0.8416 (m-30) REVERT: A 910 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7317 (tp30) REVERT: E 116 MET cc_start: 0.7771 (mtp) cc_final: 0.7493 (mtp) REVERT: E 151 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7151 (mp) REVERT: E 179 ASN cc_start: 0.7052 (p0) cc_final: 0.6817 (p0) REVERT: E 240 LYS cc_start: 0.8101 (mttt) cc_final: 0.7552 (mmtm) REVERT: F 1 MET cc_start: 0.7710 (ppp) cc_final: 0.7351 (tmm) REVERT: F 146 ARG cc_start: 0.8040 (mtt-85) cc_final: 0.7694 (mmm-85) REVERT: F 168 LYS cc_start: 0.8225 (mttt) cc_final: 0.7912 (mptt) REVERT: F 199 MET cc_start: 0.5129 (ptp) cc_final: 0.4907 (mmm) REVERT: F 215 PHE cc_start: 0.6705 (m-10) cc_final: 0.5921 (m-80) REVERT: F 248 LYS cc_start: 0.5952 (mttt) cc_final: 0.5264 (tttm) REVERT: G 75 MET cc_start: 0.6852 (ttt) cc_final: 0.5768 (mmp) REVERT: G 151 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7019 (mm) REVERT: G 229 MET cc_start: 0.4733 (mpp) cc_final: 0.4118 (mpp) REVERT: G 249 TYR cc_start: 0.5182 (m-80) cc_final: 0.4974 (m-80) outliers start: 47 outliers final: 25 residues processed: 191 average time/residue: 0.1093 time to fit residues: 29.3011 Evaluate side-chains 172 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 179 ASN Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 106 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 103 optimal weight: 0.1980 chunk 81 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 821 HIS E 71 ASN F 184 GLN G 71 ASN ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.178722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.128393 restraints weight = 18684.053| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.52 r_work: 0.3440 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 12202 Z= 0.210 Angle : 0.599 7.056 16769 Z= 0.318 Chirality : 0.043 0.178 1931 Planarity : 0.004 0.050 1913 Dihedral : 18.992 71.023 2121 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.96 % Allowed : 25.53 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.23), residues: 1319 helix: 1.42 (0.24), residues: 490 sheet: 0.14 (0.27), residues: 350 loop : -1.22 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 880 TYR 0.019 0.002 TYR E 211 PHE 0.015 0.002 PHE F 169 TRP 0.009 0.001 TRP A 638 HIS 0.006 0.001 HIS A1005 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (12201) covalent geometry : angle 0.59906 / 0.32 (16767) SS BOND : bond 0.00518 / 0.32 ( 1) SS BOND : angle 0.91039 / 0.42 ( 2) hydrogen bonds : bond 0.04502 / 2.96 ( 622) hydrogen bonds : angle 4.76885 / 3.35 ( 1712) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 145 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8013 (mtmm) REVERT: A 498 ASP cc_start: 0.8753 (m-30) cc_final: 0.8313 (m-30) REVERT: A 592 LYS cc_start: 0.8625 (mmtt) cc_final: 0.8364 (mmtt) REVERT: A 648 ARG cc_start: 0.7565 (mpt180) cc_final: 0.6878 (mmt180) REVERT: A 670 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7689 (mp) REVERT: A 715 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8215 (mp) REVERT: A 910 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7293 (tp30) REVERT: E 2 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.5768 (p90) REVERT: E 116 MET cc_start: 0.7712 (mtp) cc_final: 0.7291 (mtp) REVERT: E 125 GLN cc_start: 0.8484 (tp40) cc_final: 0.8278 (tp40) REVERT: E 179 ASN cc_start: 0.6784 (p0) cc_final: 0.6459 (p0) REVERT: E 240 LYS cc_start: 0.8155 (mttt) cc_final: 0.7555 (mmtm) REVERT: F 1 MET cc_start: 0.7750 (ppp) cc_final: 0.7361 (tmm) REVERT: F 146 ARG cc_start: 0.8132 (mtt-85) cc_final: 0.7726 (mmm160) REVERT: F 168 LYS cc_start: 0.8069 (mttt) cc_final: 0.7712 (mptt) REVERT: F 199 MET cc_start: 0.5266 (ptp) cc_final: 0.4948 (mmm) REVERT: F 215 PHE cc_start: 0.6627 (m-10) cc_final: 0.5867 (m-80) REVERT: F 248 LYS cc_start: 0.5706 (mttt) cc_final: 0.5070 (tttm) REVERT: G 75 MET cc_start: 0.6904 (ttt) cc_final: 0.5737 (mmp) REVERT: G 151 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7162 (mm) REVERT: G 229 MET cc_start: 0.4965 (mpp) cc_final: 0.4290 (mpp) outliers start: 70 outliers final: 45 residues processed: 198 average time/residue: 0.1075 time to fit residues: 29.4431 Evaluate side-chains 183 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 132 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 179 ASN Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 251 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 59 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 133 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 65 optimal weight: 20.0000 chunk 85 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.180805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.134213 restraints weight = 18588.954| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.26 r_work: 0.3518 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12202 Z= 0.133 Angle : 0.539 7.539 16769 Z= 0.289 Chirality : 0.041 0.142 1931 Planarity : 0.004 0.038 1913 Dihedral : 18.969 70.489 2118 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.19 % Allowed : 26.21 % Favored : 68.60 % 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: 0.31 (0.23), residues: 1319 helix: 1.56 (0.24), residues: 497 sheet: 0.16 (0.28), residues: 336 loop : -1.16 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 146 TYR 0.014 0.002 TYR E 211 PHE 0.010 0.001 PHE A 545 TRP 0.008 0.001 TRP A 847 HIS 0.007 0.001 HIS E 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (12201) covalent geometry : angle 0.53862 / 0.29 (16767) SS BOND : bond 0.00563 / 0.35 ( 1) SS BOND : angle 0.98341 / 0.45 ( 2) hydrogen bonds : bond 0.04038 / 2.65 ( 622) hydrogen bonds : angle 4.57602 / 3.21 ( 1712) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 144 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 ASP cc_start: 0.8783 (m-30) cc_final: 0.8329 (m-30) REVERT: A 592 LYS cc_start: 0.8700 (mmtt) cc_final: 0.8425 (mmtt) REVERT: A 648 ARG cc_start: 0.7642 (mpt180) cc_final: 0.7074 (mmt180) REVERT: A 670 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7729 (mp) REVERT: A 715 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8218 (mp) REVERT: A 869 ASP cc_start: 0.8766 (m-30) cc_final: 0.8472 (m-30) REVERT: E 2 PHE cc_start: 0.7377 (OUTLIER) cc_final: 0.5866 (p90) REVERT: E 16 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8507 (mm) REVERT: E 116 MET cc_start: 0.7718 (mtp) cc_final: 0.7291 (mtp) REVERT: E 179 ASN cc_start: 0.6823 (p0) cc_final: 0.6598 (p0) REVERT: E 198 GLU cc_start: 0.6023 (OUTLIER) cc_final: 0.5739 (pp20) REVERT: E 240 LYS cc_start: 0.8195 (mttt) cc_final: 0.7588 (mmtm) REVERT: F 146 ARG cc_start: 0.8083 (mtt-85) cc_final: 0.7665 (mmm-85) REVERT: F 168 LYS cc_start: 0.8170 (mttt) cc_final: 0.7827 (mptt) REVERT: F 199 MET cc_start: 0.5310 (ptp) cc_final: 0.4853 (mmm) REVERT: F 215 PHE cc_start: 0.6650 (m-10) cc_final: 0.5898 (m-80) REVERT: F 248 LYS cc_start: 0.5974 (mttt) cc_final: 0.5233 (tttm) outliers start: 61 outliers final: 43 residues processed: 187 average time/residue: 0.1033 time to fit residues: 27.6125 Evaluate side-chains 183 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 179 ASN Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 251 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 105 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 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 = 0.4261 r_free = 0.4261 target = 0.179165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.139921 restraints weight = 18655.566| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 3.72 r_work: 0.3370 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12202 Z= 0.185 Angle : 0.569 6.275 16769 Z= 0.303 Chirality : 0.042 0.139 1931 Planarity : 0.004 0.041 1913 Dihedral : 19.021 70.531 2117 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 6.13 % Allowed : 25.70 % Favored : 68.17 % 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: 0.26 (0.23), residues: 1319 helix: 1.49 (0.24), residues: 496 sheet: 0.17 (0.28), residues: 338 loop : -1.19 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 5 TYR 0.017 0.002 TYR E 211 PHE 0.012 0.002 PHE F 169 TRP 0.008 0.001 TRP A 638 HIS 0.007 0.001 HIS E 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (12201) covalent geometry : angle 0.56890 / 0.30 (16767) SS BOND : bond 0.00506 / 0.32 ( 1) SS BOND : angle 0.84395 / 0.39 ( 2) hydrogen bonds : bond 0.04173 / 2.75 ( 622) hydrogen bonds : angle 4.65651 / 3.26 ( 1712) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 145 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 401 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8099 (mtpt) REVERT: A 424 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.7657 (mtm-85) REVERT: A 498 ASP cc_start: 0.8754 (m-30) cc_final: 0.8310 (m-30) REVERT: A 592 LYS cc_start: 0.8705 (mmtt) cc_final: 0.8460 (mmtt) REVERT: A 648 ARG cc_start: 0.7654 (mpt180) cc_final: 0.6987 (mmt180) REVERT: A 670 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7829 (mp) REVERT: A 715 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8209 (mp) REVERT: A 910 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7307 (tp30) REVERT: E 2 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.5983 (p90) REVERT: E 116 MET cc_start: 0.7751 (mtp) cc_final: 0.7346 (mtp) REVERT: E 179 ASN cc_start: 0.6944 (p0) cc_final: 0.6571 (p0) REVERT: E 198 GLU cc_start: 0.6066 (OUTLIER) cc_final: 0.5840 (pp20) REVERT: E 235 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6368 (tp) REVERT: E 240 LYS cc_start: 0.8200 (mttt) cc_final: 0.7630 (mmtm) REVERT: F 1 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7382 (tmm) REVERT: F 146 ARG cc_start: 0.8077 (mtt-85) cc_final: 0.7697 (mmm160) REVERT: F 168 LYS cc_start: 0.8160 (mttt) cc_final: 0.7813 (mptt) REVERT: F 199 MET cc_start: 0.5270 (ptp) cc_final: 0.4801 (mmm) REVERT: F 215 PHE cc_start: 0.6719 (m-10) cc_final: 0.5955 (m-80) REVERT: F 248 LYS cc_start: 0.6090 (mttt) cc_final: 0.5335 (tttm) REVERT: G 75 MET cc_start: 0.6822 (ttt) cc_final: 0.5808 (mmp) REVERT: G 119 MET cc_start: 0.5419 (tmm) cc_final: 0.5165 (tmm) REVERT: G 199 MET cc_start: 0.3775 (mmp) cc_final: 0.0738 (tmm) REVERT: G 229 MET cc_start: 0.4625 (mpp) cc_final: 0.3490 (mpp) outliers start: 72 outliers final: 52 residues processed: 199 average time/residue: 0.1105 time to fit residues: 31.3073 Evaluate side-chains 200 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 139 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 179 ASN Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 251 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 91 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 13 optimal weight: 0.1980 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 821 HIS ** G 107 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 = 0.4277 r_free = 0.4277 target = 0.180763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.140806 restraints weight = 18664.236| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 3.53 r_work: 0.3408 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12202 Z= 0.127 Angle : 0.537 6.153 16769 Z= 0.287 Chirality : 0.041 0.137 1931 Planarity : 0.004 0.047 1913 Dihedral : 18.968 69.981 2114 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.62 % Allowed : 26.89 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.23), residues: 1319 helix: 1.66 (0.24), residues: 496 sheet: 0.11 (0.28), residues: 338 loop : -1.12 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 5 TYR 0.014 0.002 TYR E 211 PHE 0.014 0.001 PHE E 2 TRP 0.008 0.001 TRP A 708 HIS 0.005 0.001 HIS A 821 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (12201) covalent geometry : angle 0.53707 / 0.29 (16767) SS BOND : bond 0.00487 / 0.30 ( 1) SS BOND : angle 0.79950 / 0.37 ( 2) hydrogen bonds : bond 0.03917 / 2.58 ( 622) hydrogen bonds : angle 4.52226 / 3.17 ( 1712) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 144 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7915 (mtmm) REVERT: A 424 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.7683 (mtm-85) REVERT: A 498 ASP cc_start: 0.8744 (m-30) cc_final: 0.8324 (m-30) REVERT: A 592 LYS cc_start: 0.8680 (mmtt) cc_final: 0.8435 (mmtt) REVERT: A 648 ARG cc_start: 0.7624 (mpt180) cc_final: 0.7088 (mmt180) REVERT: A 649 CYS cc_start: 0.8833 (t) cc_final: 0.8378 (t) REVERT: A 670 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7725 (mp) REVERT: A 715 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8162 (mp) REVERT: A 765 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.6982 (tp) REVERT: A 950 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8129 (t70) REVERT: E 2 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.5898 (p90) REVERT: E 16 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8473 (mm) REVERT: E 116 MET cc_start: 0.7721 (mtp) cc_final: 0.7308 (mtp) REVERT: E 179 ASN cc_start: 0.6857 (p0) cc_final: 0.6502 (p0) REVERT: E 198 GLU cc_start: 0.6103 (OUTLIER) cc_final: 0.5789 (pp20) REVERT: E 199 MET cc_start: 0.5644 (mmm) cc_final: 0.5337 (mmm) REVERT: E 235 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6125 (tp) REVERT: E 240 LYS cc_start: 0.8195 (mttt) cc_final: 0.7602 (mmtm) REVERT: F 1 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7180 (tmm) REVERT: F 146 ARG cc_start: 0.8052 (mtt-85) cc_final: 0.7688 (mmm160) REVERT: F 168 LYS cc_start: 0.8131 (mttt) cc_final: 0.7782 (mptt) REVERT: F 199 MET cc_start: 0.5262 (ptp) cc_final: 0.4819 (mmm) REVERT: F 248 LYS cc_start: 0.6009 (mttt) cc_final: 0.5282 (tttm) REVERT: G 75 MET cc_start: 0.6902 (ttt) cc_final: 0.5865 (mmp) REVERT: G 119 MET cc_start: 0.5445 (tmm) cc_final: 0.5147 (tmm) REVERT: G 199 MET cc_start: 0.3455 (mmp) cc_final: 0.0481 (tmm) REVERT: G 229 MET cc_start: 0.4549 (mpp) cc_final: 0.3453 (mpp) outliers start: 66 outliers final: 44 residues processed: 191 average time/residue: 0.1216 time to fit residues: 32.2879 Evaluate side-chains 197 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 142 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 179 ASN Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 251 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 0 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 107 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 = 0.4269 r_free = 0.4269 target = 0.180000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.133348 restraints weight = 18609.062| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.30 r_work: 0.3503 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12202 Z= 0.151 Angle : 0.548 8.898 16769 Z= 0.291 Chirality : 0.041 0.137 1931 Planarity : 0.003 0.038 1913 Dihedral : 18.983 69.755 2114 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.79 % Allowed : 27.06 % Favored : 67.15 % 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: 0.36 (0.23), residues: 1319 helix: 1.65 (0.24), residues: 496 sheet: 0.11 (0.28), residues: 338 loop : -1.13 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 5 TYR 0.016 0.002 TYR G 249 PHE 0.010 0.001 PHE F 169 TRP 0.007 0.001 TRP A 638 HIS 0.003 0.001 HIS A1005 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (12201) covalent geometry : angle 0.54783 / 0.29 (16767) SS BOND : bond 0.00512 / 0.32 ( 1) SS BOND : angle 0.79763 / 0.37 ( 2) hydrogen bonds : bond 0.03953 / 2.61 ( 622) hydrogen bonds : angle 4.52696 / 3.17 ( 1712) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 146 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 401 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7919 (mtmm) REVERT: A 424 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.7658 (mtm-85) REVERT: A 498 ASP cc_start: 0.8798 (m-30) cc_final: 0.8363 (m-30) REVERT: A 592 LYS cc_start: 0.8700 (mmtt) cc_final: 0.8440 (mmtt) REVERT: A 648 ARG cc_start: 0.7651 (mpt180) cc_final: 0.7011 (mmt180) REVERT: A 649 CYS cc_start: 0.8892 (t) cc_final: 0.8439 (t) REVERT: A 670 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7744 (mp) REVERT: A 715 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8194 (mp) REVERT: A 950 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8204 (t70) REVERT: E 2 PHE cc_start: 0.7498 (OUTLIER) cc_final: 0.5865 (p90) REVERT: E 16 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8487 (mm) REVERT: E 116 MET cc_start: 0.7745 (mtp) cc_final: 0.7286 (mtp) REVERT: E 179 ASN cc_start: 0.6851 (p0) cc_final: 0.6491 (p0) REVERT: E 198 GLU cc_start: 0.6064 (OUTLIER) cc_final: 0.5803 (pp20) REVERT: E 235 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6187 (tp) REVERT: E 240 LYS cc_start: 0.8223 (mttt) cc_final: 0.7606 (mmtm) REVERT: F 1 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7172 (tmm) REVERT: F 146 ARG cc_start: 0.8108 (mtt-85) cc_final: 0.7700 (mmm160) REVERT: F 168 LYS cc_start: 0.8124 (mttt) cc_final: 0.7744 (mptt) REVERT: F 199 MET cc_start: 0.5341 (ptp) cc_final: 0.4870 (mmm) REVERT: F 215 PHE cc_start: 0.6595 (m-10) cc_final: 0.5753 (m-80) REVERT: F 248 LYS cc_start: 0.5963 (mttt) cc_final: 0.5269 (tttm) REVERT: G 75 MET cc_start: 0.6948 (ttt) cc_final: 0.5873 (mmp) REVERT: G 119 MET cc_start: 0.5503 (tmm) cc_final: 0.5199 (tmm) REVERT: G 229 MET cc_start: 0.4660 (mpp) cc_final: 0.3756 (mpp) outliers start: 68 outliers final: 52 residues processed: 198 average time/residue: 0.1267 time to fit residues: 35.2887 Evaluate side-chains 200 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 138 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 153 HIS Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 179 ASN Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 251 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 42 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 107 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 = 0.4279 r_free = 0.4279 target = 0.180891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.140737 restraints weight = 18604.092| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 3.41 r_work: 0.3421 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12202 Z= 0.128 Angle : 0.538 7.562 16769 Z= 0.286 Chirality : 0.041 0.247 1931 Planarity : 0.003 0.038 1913 Dihedral : 18.966 69.179 2114 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.79 % Allowed : 26.81 % Favored : 67.40 % 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: 0.47 (0.23), residues: 1319 helix: 1.78 (0.24), residues: 496 sheet: 0.16 (0.28), residues: 334 loop : -1.09 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 149 TYR 0.017 0.002 TYR G 249 PHE 0.008 0.001 PHE F 169 TRP 0.007 0.001 TRP A 708 HIS 0.003 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (12201) covalent geometry : angle 0.53795 / 0.29 (16767) SS BOND : bond 0.00523 / 0.33 ( 1) SS BOND : angle 0.83775 / 0.39 ( 2) hydrogen bonds : bond 0.03826 / 2.51 ( 622) hydrogen bonds : angle 4.45763 / 3.12 ( 1712) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 144 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 401 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7940 (mtmm) REVERT: A 424 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.7696 (mtm-85) REVERT: A 498 ASP cc_start: 0.8746 (m-30) cc_final: 0.8334 (m-30) REVERT: A 592 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8423 (mmtt) REVERT: A 648 ARG cc_start: 0.7637 (mpt180) cc_final: 0.7009 (mmt180) REVERT: A 649 CYS cc_start: 0.8811 (t) cc_final: 0.8350 (t) REVERT: A 670 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7730 (mp) REVERT: A 715 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8151 (mp) REVERT: A 765 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.6968 (tp) REVERT: A 950 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8132 (t70) REVERT: E 2 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.5826 (p90) REVERT: E 16 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8453 (mm) REVERT: E 116 MET cc_start: 0.7718 (mtp) cc_final: 0.7304 (mtp) REVERT: E 179 ASN cc_start: 0.6849 (p0) cc_final: 0.6513 (p0) REVERT: E 198 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.5808 (pp20) REVERT: E 199 MET cc_start: 0.5593 (mmm) cc_final: 0.5246 (mmm) REVERT: E 235 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6095 (tp) REVERT: E 240 LYS cc_start: 0.8184 (mttt) cc_final: 0.7621 (mmtm) REVERT: F 1 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7166 (tmm) REVERT: F 146 ARG cc_start: 0.8054 (mtt-85) cc_final: 0.7685 (mmm160) REVERT: F 168 LYS cc_start: 0.8124 (mttt) cc_final: 0.7774 (mptt) REVERT: F 199 MET cc_start: 0.5284 (ptp) cc_final: 0.4851 (mmm) REVERT: F 215 PHE cc_start: 0.6610 (m-10) cc_final: 0.5782 (m-80) REVERT: F 238 GLU cc_start: 0.3873 (OUTLIER) cc_final: 0.3543 (tm-30) REVERT: F 248 LYS cc_start: 0.5971 (mttt) cc_final: 0.5275 (tttm) REVERT: G 75 MET cc_start: 0.6892 (ttt) cc_final: 0.5850 (mmp) REVERT: G 119 MET cc_start: 0.5415 (tmm) cc_final: 0.5133 (tmm) REVERT: G 229 MET cc_start: 0.4492 (mpp) cc_final: 0.3588 (mpp) outliers start: 68 outliers final: 49 residues processed: 195 average time/residue: 0.1190 time to fit residues: 32.5976 Evaluate side-chains 200 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 139 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 153 HIS Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 179 ASN Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 251 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 10 optimal weight: 0.0980 chunk 76 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 0.0370 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 107 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 = 0.4281 r_free = 0.4281 target = 0.181277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.140864 restraints weight = 18435.898| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 3.27 r_work: 0.3437 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12202 Z= 0.114 Angle : 0.526 7.197 16769 Z= 0.281 Chirality : 0.040 0.137 1931 Planarity : 0.003 0.036 1913 Dihedral : 18.933 68.532 2114 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.02 % Allowed : 27.23 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.23), residues: 1319 helix: 1.89 (0.24), residues: 496 sheet: 0.24 (0.28), residues: 330 loop : -1.06 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 149 TYR 0.016 0.001 TYR G 249 PHE 0.008 0.001 PHE E 2 TRP 0.007 0.001 TRP A 708 HIS 0.003 0.001 HIS E 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (12201) covalent geometry : angle 0.52623 / 0.28 (16767) SS BOND : bond 0.00487 / 0.30 ( 1) SS BOND : angle 0.73921 / 0.34 ( 2) hydrogen bonds : bond 0.03710 / 2.44 ( 622) hydrogen bonds : angle 4.39301 / 3.07 ( 1712) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 150 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 401 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7879 (mtmm) REVERT: A 424 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.7697 (mtm-85) REVERT: A 498 ASP cc_start: 0.8746 (m-30) cc_final: 0.8367 (m-30) REVERT: A 592 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8406 (mmtt) REVERT: A 648 ARG cc_start: 0.7591 (mpt180) cc_final: 0.7033 (mmt180) REVERT: A 649 CYS cc_start: 0.8761 (t) cc_final: 0.8316 (t) REVERT: A 670 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7693 (mp) REVERT: A 765 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7002 (tp) REVERT: A 869 ASP cc_start: 0.8673 (m-30) cc_final: 0.8366 (m-30) REVERT: A 880 ARG cc_start: 0.7800 (ttp-110) cc_final: 0.7512 (ttp-110) REVERT: A 950 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8109 (t70) REVERT: E 2 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.5858 (p90) REVERT: E 16 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8381 (mm) REVERT: E 116 MET cc_start: 0.7692 (mtp) cc_final: 0.7275 (mtp) REVERT: E 179 ASN cc_start: 0.6772 (p0) cc_final: 0.6468 (p0) REVERT: E 198 GLU cc_start: 0.6136 (OUTLIER) cc_final: 0.5813 (pp20) REVERT: E 199 MET cc_start: 0.5567 (mmm) cc_final: 0.5221 (mmm) REVERT: E 240 LYS cc_start: 0.8183 (mttt) cc_final: 0.7605 (mmtm) REVERT: E 248 LYS cc_start: 0.8357 (mttt) cc_final: 0.8053 (mttm) REVERT: F 1 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7151 (tmm) REVERT: F 30 ILE cc_start: 0.6880 (tp) cc_final: 0.6536 (mm) REVERT: F 49 GLN cc_start: 0.6300 (tp40) cc_final: 0.4845 (tm-30) REVERT: F 146 ARG cc_start: 0.8034 (mtt-85) cc_final: 0.7683 (mmm160) REVERT: F 168 LYS cc_start: 0.8132 (mttt) cc_final: 0.7708 (mptt) REVERT: F 199 MET cc_start: 0.5258 (ptp) cc_final: 0.4835 (mmm) REVERT: F 238 GLU cc_start: 0.3832 (OUTLIER) cc_final: 0.3500 (tm-30) REVERT: F 248 LYS cc_start: 0.5866 (mttt) cc_final: 0.5089 (tttm) REVERT: G 17 GLU cc_start: 0.8167 (pt0) cc_final: 0.7533 (pp20) REVERT: G 75 MET cc_start: 0.6884 (ttt) cc_final: 0.5844 (mmp) REVERT: G 119 MET cc_start: 0.5497 (tmm) cc_final: 0.5231 (tmm) REVERT: G 229 MET cc_start: 0.4664 (mpp) cc_final: 0.3835 (mpp) outliers start: 59 outliers final: 43 residues processed: 195 average time/residue: 0.1123 time to fit residues: 30.9513 Evaluate side-chains 202 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 149 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 153 HIS Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 179 ASN Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 251 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 99 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 23 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 137 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 107 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 = 0.4275 r_free = 0.4275 target = 0.180501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.133948 restraints weight = 18641.986| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.30 r_work: 0.3509 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12202 Z= 0.141 Angle : 0.547 7.368 16769 Z= 0.291 Chirality : 0.041 0.138 1931 Planarity : 0.003 0.038 1913 Dihedral : 18.962 68.279 2114 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.77 % Allowed : 28.00 % Favored : 67.23 % 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: 0.47 (0.23), residues: 1319 helix: 1.81 (0.24), residues: 498 sheet: 0.14 (0.28), residues: 333 loop : -1.13 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 149 TYR 0.018 0.002 TYR G 249 PHE 0.010 0.001 PHE F 169 TRP 0.007 0.001 TRP A 638 HIS 0.003 0.001 HIS A1005 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (12201) covalent geometry : angle 0.54667 / 0.29 (16767) SS BOND : bond 0.00375 / 0.23 ( 1) SS BOND : angle 0.61426 / 0.29 ( 2) hydrogen bonds : bond 0.03828 / 2.52 ( 622) hydrogen bonds : angle 4.47401 / 3.13 ( 1712) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 147 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8064 (mtmt) REVERT: A 424 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.7656 (mtm-85) REVERT: A 498 ASP cc_start: 0.8791 (m-30) cc_final: 0.8357 (m-30) REVERT: A 592 LYS cc_start: 0.8709 (mmtt) cc_final: 0.8436 (mmtt) REVERT: A 648 ARG cc_start: 0.7651 (mpt180) cc_final: 0.7027 (mmt180) REVERT: A 649 CYS cc_start: 0.8856 (t) cc_final: 0.8421 (t) REVERT: A 670 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7695 (mp) REVERT: A 765 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7035 (tp) REVERT: A 880 ARG cc_start: 0.7885 (ttp-110) cc_final: 0.7546 (ttp-110) REVERT: A 950 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8229 (t70) REVERT: E 2 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.5794 (p90) REVERT: E 16 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8446 (mm) REVERT: E 40 MET cc_start: 0.8012 (ttm) cc_final: 0.7787 (mtp) REVERT: E 116 MET cc_start: 0.7712 (mtp) cc_final: 0.7266 (mtp) REVERT: E 179 ASN cc_start: 0.6788 (p0) cc_final: 0.6479 (p0) REVERT: E 198 GLU cc_start: 0.6088 (OUTLIER) cc_final: 0.5747 (pp20) REVERT: E 199 MET cc_start: 0.5573 (mmm) cc_final: 0.5178 (mmm) REVERT: E 240 LYS cc_start: 0.8229 (mttt) cc_final: 0.7618 (mmtm) REVERT: F 1 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7161 (tmm) REVERT: F 30 ILE cc_start: 0.6910 (tp) cc_final: 0.6567 (mm) REVERT: F 49 GLN cc_start: 0.6311 (tp40) cc_final: 0.4837 (tm-30) REVERT: F 146 ARG cc_start: 0.8093 (mtt-85) cc_final: 0.7693 (mmm160) REVERT: F 168 LYS cc_start: 0.8120 (mttt) cc_final: 0.7669 (mptt) REVERT: F 199 MET cc_start: 0.5303 (ptp) cc_final: 0.4856 (mmm) REVERT: F 215 PHE cc_start: 0.6464 (m-10) cc_final: 0.5706 (m-80) REVERT: F 238 GLU cc_start: 0.3860 (OUTLIER) cc_final: 0.3514 (tm-30) REVERT: F 248 LYS cc_start: 0.5885 (mttt) cc_final: 0.5090 (tttm) REVERT: G 17 GLU cc_start: 0.8144 (pt0) cc_final: 0.7532 (pp20) REVERT: G 75 MET cc_start: 0.6876 (ttt) cc_final: 0.5846 (mmp) REVERT: G 119 MET cc_start: 0.5628 (tmm) cc_final: 0.5358 (tmm) REVERT: G 229 MET cc_start: 0.4870 (mpp) cc_final: 0.3977 (mpp) outliers start: 56 outliers final: 44 residues processed: 191 average time/residue: 0.1114 time to fit residues: 29.5901 Evaluate side-chains 198 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 144 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 153 HIS Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 179 ASN Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 251 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 61 optimal weight: 30.0000 chunk 62 optimal weight: 30.0000 chunk 87 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 107 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 = 0.4277 r_free = 0.4277 target = 0.180635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.134253 restraints weight = 18623.214| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.29 r_work: 0.3511 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12202 Z= 0.135 Angle : 0.547 7.608 16769 Z= 0.290 Chirality : 0.041 0.138 1931 Planarity : 0.003 0.037 1913 Dihedral : 18.963 67.902 2114 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.11 % Allowed : 27.66 % Favored : 67.23 % 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: 0.47 (0.23), residues: 1319 helix: 1.82 (0.24), residues: 498 sheet: 0.12 (0.28), residues: 333 loop : -1.13 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 149 TYR 0.018 0.002 TYR G 249 PHE 0.009 0.001 PHE F 169 TRP 0.007 0.001 TRP A 638 HIS 0.003 0.001 HIS E 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (12201) covalent geometry : angle 0.54677 / 0.29 (16767) SS BOND : bond 0.00446 / 0.28 ( 1) SS BOND : angle 0.82113 / 0.39 ( 2) hydrogen bonds : bond 0.03786 / 2.50 ( 622) hydrogen bonds : angle 4.45459 / 3.12 ( 1712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2882.42 seconds wall clock time: 50 minutes 8.41 seconds (3008.41 seconds total)