Starting phenix.real_space_refine on Fri Jul 3 12:06:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7k_38101/07_2026/8x7k_38101.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7k_38101/07_2026/8x7k_38101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x7k_38101/07_2026/8x7k_38101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7k_38101/07_2026/8x7k_38101.map" model { file = "/net/cci-nas-00/data/ceres_data/8x7k_38101/07_2026/8x7k_38101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7k_38101/07_2026/8x7k_38101.cif" } resolution = 3.27 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1133 atoms to isotropic. 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 Zn 2 6.06 5 P 286 5.49 5 S 24 5.16 5 C 7527 2.51 5 N 2489 2.21 5 O 3059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 13387 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 794 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 642 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 803 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2948 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "J" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2915 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "K" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1139 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 128} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 400 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'TRP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13109 SG CYS L 31 60.059 69.150 26.494 1.00258.38 S ATOM 13259 SG CYS L 51 62.331 72.122 26.337 1.00256.92 S ATOM 13283 SG CYS L 54 58.552 72.626 25.943 1.00257.61 S ATOM 13000 SG CYS L 16 72.742 69.224 21.927 1.00277.18 S ATOM 13018 SG CYS L 19 76.269 68.875 20.741 1.00278.85 S ATOM 13148 SG CYS L 36 75.177 66.760 23.539 1.00279.94 S ATOM 13170 SG CYS L 39 75.610 70.474 24.195 1.00280.00 S Time building chain proxies: 3.00, per 1000 atoms: 0.22 Number of scatterers: 13387 At special positions: 0 Unit cell: (118.14, 125.658, 114.918, 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) Zn 2 29.99 S 24 16.00 P 286 15.00 O 3059 8.00 N 2489 7.00 C 7527 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 459.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" ND1 HIS L 33 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 54 " pdb=" ZN L 202 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 16 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 39 " Number of angles added : 9 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1796 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 12 sheets defined 66.0% alpha, 4.4% beta 144 base pairs and 239 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 77 removed outlier: 3.837A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.475A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.368A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.602A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 29 removed outlier: 3.816A pdb=" N ASN F 25 " --> pdb=" O LEU F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.964A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.615A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.538A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'K' and resid 2 through 16 Processing helix chain 'K' and resid 86 through 91 Processing helix chain 'K' and resid 98 through 112 Processing helix chain 'K' and resid 120 through 130 Processing helix chain 'K' and resid 130 through 146 Processing helix chain 'L' and resid 36 through 44 Processing helix chain 'L' and resid 58 through 67 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.777A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.573A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.644A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.040A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.361A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 22 through 25 Processing sheet with id=AB3, first strand: chain 'L' and resid 27 through 28 477 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 602 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 239 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2956 1.33 - 1.45: 4165 1.45 - 1.57: 6488 1.57 - 1.69: 570 1.69 - 1.81: 38 Bond restraints: 14217 Sorted by residual: bond pdb=" C3' DT J -39 " pdb=" C2' DT J -39 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DC I 52 " pdb=" C2' DC I 52 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.94e+00 bond pdb=" C3' DG I 29 " pdb=" C2' DG I 29 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.69e+00 bond pdb=" C3' DA J -22 " pdb=" C2' DA J -22 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.40e+00 bond pdb=" C3' DT I -29 " pdb=" C2' DT I -29 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.21e+00 ... (remaining 14212 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 18283 1.10 - 2.20: 1692 2.20 - 3.30: 435 3.30 - 4.40: 31 4.40 - 5.50: 8 Bond angle restraints: 20449 Sorted by residual: angle pdb=" O4' DA J 32 " pdb=" C4' DA J 32 " pdb=" C3' DA J 32 " ideal model delta sigma weight residual 106.00 102.55 3.45 6.00e-01 2.78e+00 3.30e+01 angle pdb=" N3 DT J 64 " pdb=" C4 DT J 64 " pdb=" O4 DT J 64 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT J 41 " pdb=" C4 DT J 41 " pdb=" O4 DT J 41 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" O4' DG I -35 " pdb=" C4' DG I -35 " pdb=" C3' DG I -35 " ideal model delta sigma weight residual 106.00 103.39 2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT I -24 " pdb=" C4 DT I -24 " pdb=" O4 DT I -24 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 ... (remaining 20444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.71: 6416 33.71 - 67.43: 1389 67.43 - 101.14: 20 101.14 - 134.85: 1 134.85 - 168.57: 2 Dihedral angle restraints: 7828 sinusoidal: 5053 harmonic: 2775 Sorted by residual: dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual -140.00 28.57 -168.57 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 56.30 163.70 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 87.88 132.12 1 3.50e+01 8.16e-04 1.31e+01 ... (remaining 7825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1625 0.041 - 0.081: 482 0.081 - 0.122: 202 0.122 - 0.163: 20 0.163 - 0.204: 1 Chirality restraints: 2330 Sorted by residual: chirality pdb=" C3' DT I -59 " pdb=" C4' DT I -59 " pdb=" O3' DT I -59 " pdb=" C2' DT I -59 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C3' DG J 40 " pdb=" C4' DG J 40 " pdb=" O3' DG J 40 " pdb=" C2' DG J 40 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" C3' DA J 17 " pdb=" C4' DA J 17 " pdb=" O3' DA J 17 " pdb=" C2' DA J 17 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 2327 not shown) Planarity restraints: 1602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I -35 " -0.023 2.00e-02 2.50e+03 9.60e-03 2.76e+00 pdb=" N9 DG I -35 " 0.020 2.00e-02 2.50e+03 pdb=" C8 DG I -35 " 0.007 2.00e-02 2.50e+03 pdb=" N7 DG I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG I -35 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I -35 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG I -35 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I -35 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I -35 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG I -35 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO D 103 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO H 103 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " -0.021 5.00e-02 4.00e+02 ... (remaining 1599 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 181 2.59 - 3.17: 10898 3.17 - 3.75: 25581 3.75 - 4.32: 32661 4.32 - 4.90: 47725 Nonbonded interactions: 117046 Sorted by model distance: nonbonded pdb=" N2 DG I -21 " pdb=" O2 DC J 21 " model vdw 2.018 2.496 nonbonded pdb=" N2 DG I 46 " pdb=" O2 DC J -46 " model vdw 2.039 2.496 nonbonded pdb=" N2 DG I 56 " pdb=" O2 DC J -56 " model vdw 2.044 2.496 nonbonded pdb=" N2 DG I -56 " pdb=" O2 DC J 56 " model vdw 2.048 2.496 nonbonded pdb=" N2 DG I 0 " pdb=" O2 DC J 0 " model vdw 2.053 2.496 ... (remaining 117041 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = (chain 'C' and (resid 14 or resid 16 through 117)) selection = (chain 'G' and (resid 14 or resid 16 through 117)) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 31 through 123) } 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.160 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 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 : 0.006 0.047 14225 Z= 0.528 Angle : 0.703 5.498 20458 Z= 0.616 Chirality : 0.045 0.204 2330 Planarity : 0.003 0.041 1602 Dihedral : 26.210 168.568 6032 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.37 % Allowed : 5.24 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.99 (0.28), residues: 932 helix: 2.88 (0.21), residues: 622 sheet: 0.69 (1.12), residues: 22 loop : 0.05 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 67 TYR 0.009 0.001 TYR K 127 PHE 0.008 0.001 PHE A 67 TRP 0.009 0.001 TRP K 93 HIS 0.004 0.001 HIS L 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.53 (14217) covalent geometry : angle 0.70148 / 0.62 (20449) hydrogen bonds : bond 0.11132 / 7.31 ( 824) hydrogen bonds : angle 3.96818 / 2.76 ( 2006) metal coordination : bond 0.00950 / 0.64 ( 8) metal coordination : angle 2.56743 / 1.94 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 262 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7277 (m-80) cc_final: 0.6725 (m-80) REVERT: A 59 GLU cc_start: 0.8455 (pt0) cc_final: 0.8234 (pt0) REVERT: A 94 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8271 (mm-30) REVERT: A 120 MET cc_start: 0.8653 (mtm) cc_final: 0.8445 (mtm) REVERT: B 95 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8278 (mtt90) REVERT: C 56 GLU cc_start: 0.8498 (tt0) cc_final: 0.8188 (tt0) REVERT: C 68 ASN cc_start: 0.8798 (m-40) cc_final: 0.8593 (m-40) REVERT: C 72 ASP cc_start: 0.8517 (m-30) cc_final: 0.8289 (m-30) REVERT: C 76 THR cc_start: 0.9124 (p) cc_final: 0.8765 (t) REVERT: C 90 ASP cc_start: 0.8515 (t70) cc_final: 0.8225 (t0) REVERT: C 92 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8281 (mm-30) REVERT: D 34 LYS cc_start: 0.8509 (ptpt) cc_final: 0.8234 (tptt) REVERT: D 68 ASP cc_start: 0.8926 (t70) cc_final: 0.8613 (t0) REVERT: D 83 TYR cc_start: 0.7991 (m-10) cc_final: 0.7418 (m-80) REVERT: D 105 GLU cc_start: 0.7765 (tp30) cc_final: 0.7329 (tp30) REVERT: D 108 LYS cc_start: 0.8708 (mtpm) cc_final: 0.8399 (ttpt) REVERT: E 54 TYR cc_start: 0.9385 (m-80) cc_final: 0.9059 (m-80) REVERT: F 77 LYS cc_start: 0.9052 (mttt) cc_final: 0.8704 (mtpp) REVERT: G 24 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8386 (mm-40) REVERT: G 39 TYR cc_start: 0.9360 (m-80) cc_final: 0.8503 (m-80) REVERT: G 56 GLU cc_start: 0.8428 (tt0) cc_final: 0.7857 (tt0) REVERT: G 89 ASN cc_start: 0.9128 (m-40) cc_final: 0.8615 (m-40) REVERT: G 92 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8069 (mm-30) REVERT: G 95 LYS cc_start: 0.9367 (ttpt) cc_final: 0.9135 (tttm) REVERT: H 68 ASP cc_start: 0.9073 (t70) cc_final: 0.8834 (t0) REVERT: H 83 TYR cc_start: 0.8059 (m-10) cc_final: 0.7416 (m-80) REVERT: H 121 TYR cc_start: 0.8988 (t80) cc_final: 0.8786 (t80) REVERT: K 34 GLN cc_start: 0.8745 (tt0) cc_final: 0.8241 (tm-30) REVERT: K 45 TYR cc_start: 0.6101 (m-80) cc_final: 0.5551 (m-80) REVERT: K 51 PHE cc_start: 0.9296 (m-80) cc_final: 0.9050 (m-80) REVERT: K 87 ASP cc_start: 0.8350 (p0) cc_final: 0.8107 (p0) REVERT: K 117 ASP cc_start: 0.6617 (t0) cc_final: 0.6283 (p0) REVERT: K 143 GLN cc_start: 0.8645 (mt0) cc_final: 0.8297 (mp10) REVERT: L 29 LEU cc_start: 0.7001 (mt) cc_final: 0.6753 (tp) REVERT: L 43 THR cc_start: 0.7501 (t) cc_final: 0.6975 (t) REVERT: L 46 LYS cc_start: 0.9220 (mtmt) cc_final: 0.8731 (ptpt) outliers start: 19 outliers final: 3 residues processed: 274 average time/residue: 0.1705 time to fit residues: 61.4673 Evaluate side-chains 197 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 193 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain F residue 50 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 20.0000 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN C 24 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS G 38 ASN G 68 ASN G 104 GLN K 7 ASN L 41 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.074597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.046539 restraints weight = 60675.353| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.75 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 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 : 0.004 0.069 14225 Z= 0.201 Angle : 0.660 10.690 20458 Z= 0.383 Chirality : 0.044 0.357 2330 Planarity : 0.005 0.072 1602 Dihedral : 30.464 165.177 4186 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.62 % Allowed : 10.61 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.27), residues: 932 helix: 2.67 (0.20), residues: 626 sheet: 0.37 (1.09), residues: 22 loop : -0.12 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 55 TYR 0.027 0.002 TYR K 74 PHE 0.019 0.002 PHE K 69 TRP 0.014 0.001 TRP K 93 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.20 (14217) covalent geometry : angle 0.64637 / 0.38 (20449) hydrogen bonds : bond 0.08830 / 6.25 ( 824) hydrogen bonds : angle 3.54954 / 2.51 ( 2006) metal coordination : bond 0.02759 / 1.57 ( 8) metal coordination : angle 6.39495 / 5.54 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.6981 (m-80) cc_final: 0.6441 (m-80) REVERT: A 120 MET cc_start: 0.8635 (mtm) cc_final: 0.8378 (mtm) REVERT: B 22 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7278 (pp) REVERT: B 88 TYR cc_start: 0.8902 (m-10) cc_final: 0.7609 (m-10) REVERT: C 56 GLU cc_start: 0.8335 (tt0) cc_final: 0.7948 (tt0) REVERT: C 68 ASN cc_start: 0.8770 (m-40) cc_final: 0.8545 (m-40) REVERT: C 76 THR cc_start: 0.9148 (p) cc_final: 0.8780 (t) REVERT: C 90 ASP cc_start: 0.8721 (t70) cc_final: 0.8483 (t70) REVERT: D 34 LYS cc_start: 0.8516 (ptpt) cc_final: 0.8176 (tptt) REVERT: D 68 ASP cc_start: 0.8965 (t70) cc_final: 0.8720 (t0) REVERT: D 71 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8225 (mm-30) REVERT: D 83 TYR cc_start: 0.7940 (m-10) cc_final: 0.7537 (m-80) REVERT: D 105 GLU cc_start: 0.7858 (tp30) cc_final: 0.7403 (tp30) REVERT: D 108 LYS cc_start: 0.8785 (mtpm) cc_final: 0.8545 (ttpt) REVERT: E 54 TYR cc_start: 0.9370 (m-80) cc_final: 0.9071 (m-80) REVERT: F 77 LYS cc_start: 0.9118 (mttt) cc_final: 0.8780 (mtpp) REVERT: G 24 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8443 (mp10) REVERT: G 56 GLU cc_start: 0.8561 (tt0) cc_final: 0.8019 (tt0) REVERT: G 89 ASN cc_start: 0.9154 (m-40) cc_final: 0.8689 (m-40) REVERT: G 90 ASP cc_start: 0.8554 (t70) cc_final: 0.8313 (t70) REVERT: G 92 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8157 (mm-30) REVERT: G 95 LYS cc_start: 0.9365 (ttpt) cc_final: 0.9141 (tttm) REVERT: H 68 ASP cc_start: 0.9087 (t70) cc_final: 0.8874 (t0) REVERT: H 83 TYR cc_start: 0.7924 (m-10) cc_final: 0.7486 (m-80) REVERT: K 34 GLN cc_start: 0.8570 (tt0) cc_final: 0.7821 (tm-30) REVERT: K 46 GLN cc_start: 0.7234 (pt0) cc_final: 0.6985 (pt0) REVERT: K 87 ASP cc_start: 0.8764 (p0) cc_final: 0.8479 (p0) REVERT: K 117 ASP cc_start: 0.6770 (t0) cc_final: 0.6429 (p0) REVERT: K 143 GLN cc_start: 0.8851 (mt0) cc_final: 0.8603 (mp10) REVERT: L 43 THR cc_start: 0.7433 (t) cc_final: 0.7064 (t) outliers start: 21 outliers final: 15 residues processed: 212 average time/residue: 0.1313 time to fit residues: 38.5153 Evaluate side-chains 204 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain K residue 37 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 82 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 115 optimal weight: 0.0770 chunk 77 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS L 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.075161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.047148 restraints weight = 61130.781| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.85 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14225 Z= 0.147 Angle : 0.614 8.915 20458 Z= 0.365 Chirality : 0.042 0.362 2330 Planarity : 0.004 0.041 1602 Dihedral : 30.391 165.937 4182 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.37 % Allowed : 11.61 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.27), residues: 932 helix: 2.82 (0.20), residues: 625 sheet: 0.42 (1.02), residues: 22 loop : -0.18 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 99 TYR 0.020 0.001 TYR K 134 PHE 0.018 0.002 PHE K 62 TRP 0.003 0.001 TRP K 33 HIS 0.002 0.001 HIS K 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.15 (14217) covalent geometry : angle 0.60617 / 0.36 (20449) hydrogen bonds : bond 0.08399 / 6.01 ( 824) hydrogen bonds : angle 3.29796 / 2.32 ( 2006) metal coordination : bond 0.00714 / 0.47 ( 8) metal coordination : angle 4.75221 / 4.14 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7040 (m-80) cc_final: 0.6576 (m-80) REVERT: A 120 MET cc_start: 0.8525 (mtm) cc_final: 0.8218 (mtm) REVERT: C 56 GLU cc_start: 0.8248 (tt0) cc_final: 0.7894 (tt0) REVERT: C 76 THR cc_start: 0.9154 (p) cc_final: 0.8777 (t) REVERT: C 90 ASP cc_start: 0.8742 (t70) cc_final: 0.8427 (t70) REVERT: D 34 LYS cc_start: 0.8489 (ptpt) cc_final: 0.8155 (tptt) REVERT: D 68 ASP cc_start: 0.8929 (t70) cc_final: 0.8716 (t0) REVERT: D 71 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8209 (mm-30) REVERT: D 83 TYR cc_start: 0.7934 (m-10) cc_final: 0.7474 (m-80) REVERT: D 105 GLU cc_start: 0.7795 (tp30) cc_final: 0.7261 (tp30) REVERT: D 108 LYS cc_start: 0.8687 (mtpm) cc_final: 0.8309 (ttpt) REVERT: E 54 TYR cc_start: 0.9341 (m-80) cc_final: 0.9015 (m-80) REVERT: F 77 LYS cc_start: 0.9103 (mttt) cc_final: 0.8771 (mtpp) REVERT: G 24 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8361 (mp10) REVERT: G 56 GLU cc_start: 0.8585 (tt0) cc_final: 0.8046 (tt0) REVERT: G 89 ASN cc_start: 0.9181 (m-40) cc_final: 0.8750 (m-40) REVERT: G 92 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8150 (mm-30) REVERT: G 95 LYS cc_start: 0.9352 (ttpt) cc_final: 0.9119 (tttm) REVERT: H 68 ASP cc_start: 0.9049 (t70) cc_final: 0.8674 (t0) REVERT: H 72 ARG cc_start: 0.9059 (mtt180) cc_final: 0.8834 (mtt180) REVERT: K 87 ASP cc_start: 0.8690 (p0) cc_final: 0.8223 (t0) REVERT: L 43 THR cc_start: 0.7329 (t) cc_final: 0.6843 (t) outliers start: 19 outliers final: 12 residues processed: 214 average time/residue: 0.1247 time to fit residues: 37.4220 Evaluate side-chains 205 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 62 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 13 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 chunk 109 optimal weight: 0.4980 chunk 32 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.074664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.046776 restraints weight = 60832.034| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.74 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14225 Z= 0.178 Angle : 0.633 9.961 20458 Z= 0.369 Chirality : 0.042 0.357 2330 Planarity : 0.004 0.043 1602 Dihedral : 30.445 166.407 4180 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.62 % Allowed : 13.11 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.27), residues: 932 helix: 2.83 (0.20), residues: 626 sheet: 0.41 (1.04), residues: 22 loop : -0.19 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 99 TYR 0.010 0.001 TYR H 83 PHE 0.011 0.001 PHE A 67 TRP 0.005 0.001 TRP K 93 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.18 (14217) covalent geometry : angle 0.62487 / 0.37 (20449) hydrogen bonds : bond 0.08380 / 5.98 ( 824) hydrogen bonds : angle 3.31950 / 2.33 ( 2006) metal coordination : bond 0.01117 / 0.71 ( 8) metal coordination : angle 4.80919 / 4.17 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7098 (m-80) cc_final: 0.6679 (m-80) REVERT: A 120 MET cc_start: 0.8588 (mtm) cc_final: 0.8284 (mtm) REVERT: B 88 TYR cc_start: 0.8893 (m-10) cc_final: 0.7670 (m-10) REVERT: C 56 GLU cc_start: 0.8288 (tt0) cc_final: 0.7931 (tt0) REVERT: C 90 ASP cc_start: 0.8744 (t70) cc_final: 0.8437 (t70) REVERT: D 34 LYS cc_start: 0.8485 (ptpt) cc_final: 0.8122 (tptt) REVERT: D 68 ASP cc_start: 0.8922 (t70) cc_final: 0.8695 (t0) REVERT: D 71 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8226 (mm-30) REVERT: D 83 TYR cc_start: 0.7842 (m-10) cc_final: 0.7523 (m-10) REVERT: D 105 GLU cc_start: 0.7831 (tp30) cc_final: 0.7252 (tp30) REVERT: D 108 LYS cc_start: 0.8711 (mtpm) cc_final: 0.8307 (ttpt) REVERT: E 54 TYR cc_start: 0.9364 (m-80) cc_final: 0.8997 (m-80) REVERT: F 77 LYS cc_start: 0.9110 (mttt) cc_final: 0.8785 (mtpp) REVERT: F 88 TYR cc_start: 0.8796 (m-10) cc_final: 0.8122 (m-10) REVERT: G 24 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8518 (mp10) REVERT: G 56 GLU cc_start: 0.8594 (tt0) cc_final: 0.8085 (tt0) REVERT: G 89 ASN cc_start: 0.9194 (m-40) cc_final: 0.8735 (m-40) REVERT: G 92 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8092 (mm-30) REVERT: G 95 LYS cc_start: 0.9354 (ttpt) cc_final: 0.9120 (tttm) REVERT: H 83 TYR cc_start: 0.8074 (m-10) cc_final: 0.7298 (m-10) REVERT: K 38 MET cc_start: 0.7932 (mpp) cc_final: 0.7270 (tmm) REVERT: K 87 ASP cc_start: 0.8669 (p0) cc_final: 0.8225 (t0) REVERT: L 43 THR cc_start: 0.7271 (t) cc_final: 0.6858 (t) outliers start: 21 outliers final: 14 residues processed: 203 average time/residue: 0.1319 time to fit residues: 37.3877 Evaluate side-chains 193 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 62 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 83 optimal weight: 30.0000 chunk 3 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 chunk 89 optimal weight: 30.0000 chunk 109 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.074231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.046337 restraints weight = 61085.823| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.70 r_work: 0.2684 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14225 Z= 0.196 Angle : 0.643 9.582 20458 Z= 0.372 Chirality : 0.043 0.354 2330 Planarity : 0.004 0.041 1602 Dihedral : 30.524 166.596 4180 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.50 % Allowed : 14.36 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.28), residues: 932 helix: 2.71 (0.21), residues: 632 sheet: 0.66 (1.09), residues: 22 loop : -0.16 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 79 TYR 0.031 0.002 TYR K 74 PHE 0.022 0.002 PHE K 62 TRP 0.005 0.001 TRP K 93 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.20 (14217) covalent geometry : angle 0.63509 / 0.37 (20449) hydrogen bonds : bond 0.08357 / 5.96 ( 824) hydrogen bonds : angle 3.34035 / 2.35 ( 2006) metal coordination : bond 0.01178 / 0.76 ( 8) metal coordination : angle 4.87347 / 4.15 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7595 (mtp85) REVERT: A 120 MET cc_start: 0.8942 (mtm) cc_final: 0.8695 (mtm) REVERT: C 56 GLU cc_start: 0.8977 (tt0) cc_final: 0.8661 (tt0) REVERT: C 90 ASP cc_start: 0.8925 (t70) cc_final: 0.8663 (t70) REVERT: D 34 LYS cc_start: 0.8442 (ptpt) cc_final: 0.8057 (tptt) REVERT: D 68 ASP cc_start: 0.9227 (t70) cc_final: 0.9009 (t0) REVERT: D 83 TYR cc_start: 0.8159 (m-10) cc_final: 0.7781 (m-10) REVERT: E 54 TYR cc_start: 0.9451 (m-80) cc_final: 0.9111 (m-80) REVERT: F 77 LYS cc_start: 0.9291 (mttt) cc_final: 0.8984 (mtpp) REVERT: F 88 TYR cc_start: 0.9176 (m-10) cc_final: 0.8680 (m-10) REVERT: G 24 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8576 (mp10) REVERT: G 56 GLU cc_start: 0.9136 (tt0) cc_final: 0.8684 (tt0) REVERT: G 89 ASN cc_start: 0.9252 (m-40) cc_final: 0.8784 (m-40) REVERT: G 92 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8152 (mm-30) REVERT: G 95 LYS cc_start: 0.9431 (ttpt) cc_final: 0.9177 (tttm) REVERT: H 83 TYR cc_start: 0.8251 (m-10) cc_final: 0.7632 (m-10) REVERT: K 92 GLN cc_start: 0.8911 (tp40) cc_final: 0.8432 (mp10) REVERT: L 43 THR cc_start: 0.7366 (t) cc_final: 0.6872 (t) outliers start: 20 outliers final: 15 residues processed: 195 average time/residue: 0.1192 time to fit residues: 32.4342 Evaluate side-chains 191 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 62 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 53 optimal weight: 30.0000 chunk 42 optimal weight: 0.5980 chunk 81 optimal weight: 20.0000 chunk 20 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS D 84 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.075131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.047138 restraints weight = 60312.750| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.80 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14225 Z= 0.139 Angle : 0.623 14.898 20458 Z= 0.362 Chirality : 0.042 0.364 2330 Planarity : 0.004 0.043 1602 Dihedral : 30.443 166.787 4180 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.00 % Allowed : 15.36 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.28), residues: 932 helix: 2.79 (0.21), residues: 631 sheet: 0.32 (1.05), residues: 24 loop : -0.13 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 79 TYR 0.024 0.001 TYR K 74 PHE 0.013 0.001 PHE A 67 TRP 0.005 0.001 TRP K 141 HIS 0.002 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.14 (14217) covalent geometry : angle 0.61540 / 0.36 (20449) hydrogen bonds : bond 0.08375 / 6.01 ( 824) hydrogen bonds : angle 3.16800 / 2.22 ( 2006) metal coordination : bond 0.00572 / 0.38 ( 8) metal coordination : angle 4.58607 / 3.91 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8492 (mtm) cc_final: 0.8149 (mtm) REVERT: C 56 GLU cc_start: 0.8276 (tt0) cc_final: 0.7923 (tt0) REVERT: C 76 THR cc_start: 0.9168 (p) cc_final: 0.8759 (t) REVERT: C 90 ASP cc_start: 0.8678 (t70) cc_final: 0.8341 (t70) REVERT: D 34 LYS cc_start: 0.8460 (ptpt) cc_final: 0.8099 (tptt) REVERT: D 68 ASP cc_start: 0.8926 (t70) cc_final: 0.8715 (t0) REVERT: D 83 TYR cc_start: 0.7852 (m-10) cc_final: 0.7632 (m-10) REVERT: E 54 TYR cc_start: 0.9340 (m-80) cc_final: 0.8942 (m-80) REVERT: F 77 LYS cc_start: 0.9163 (mttt) cc_final: 0.8834 (mtpp) REVERT: F 88 TYR cc_start: 0.8879 (m-10) cc_final: 0.8163 (m-10) REVERT: G 56 GLU cc_start: 0.8584 (tt0) cc_final: 0.8063 (tt0) REVERT: G 89 ASN cc_start: 0.9220 (m-40) cc_final: 0.8756 (m-40) REVERT: G 92 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8081 (mm-30) REVERT: G 95 LYS cc_start: 0.9342 (ttpt) cc_final: 0.9092 (tttm) REVERT: H 83 TYR cc_start: 0.8164 (m-10) cc_final: 0.7482 (m-10) REVERT: K 1 MET cc_start: 0.5505 (mmt) cc_final: 0.5222 (tpp) REVERT: K 46 GLN cc_start: 0.8759 (pp30) cc_final: 0.8551 (pm20) REVERT: K 92 GLN cc_start: 0.8866 (tp40) cc_final: 0.8486 (mp10) REVERT: L 29 LEU cc_start: 0.7084 (mt) cc_final: 0.6787 (tp) REVERT: L 43 THR cc_start: 0.7158 (t) cc_final: 0.6738 (t) outliers start: 16 outliers final: 10 residues processed: 209 average time/residue: 0.1081 time to fit residues: 31.9675 Evaluate side-chains 195 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 185 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain L residue 35 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 77 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 6 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 87 optimal weight: 50.0000 chunk 13 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.074552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.046566 restraints weight = 60886.192| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.76 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14225 Z= 0.179 Angle : 0.639 11.401 20458 Z= 0.368 Chirality : 0.042 0.356 2330 Planarity : 0.004 0.047 1602 Dihedral : 30.510 167.575 4180 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.00 % Allowed : 16.48 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.28), residues: 932 helix: 2.76 (0.20), residues: 632 sheet: 0.25 (1.01), residues: 24 loop : -0.12 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 79 TYR 0.020 0.002 TYR K 74 PHE 0.012 0.001 PHE A 67 TRP 0.005 0.001 TRP K 93 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.18 (14217) covalent geometry : angle 0.63194 / 0.37 (20449) hydrogen bonds : bond 0.08256 / 5.90 ( 824) hydrogen bonds : angle 3.24757 / 2.28 ( 2006) metal coordination : bond 0.00907 / 0.60 ( 8) metal coordination : angle 4.50679 / 3.86 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8573 (mtm) cc_final: 0.8259 (mtm) REVERT: C 56 GLU cc_start: 0.8314 (tt0) cc_final: 0.7956 (tt0) REVERT: C 90 ASP cc_start: 0.8725 (t70) cc_final: 0.8342 (t70) REVERT: D 34 LYS cc_start: 0.8448 (ptpt) cc_final: 0.8049 (tptt) REVERT: D 68 ASP cc_start: 0.8946 (t70) cc_final: 0.8712 (t0) REVERT: D 83 TYR cc_start: 0.7810 (m-10) cc_final: 0.7562 (m-10) REVERT: F 77 LYS cc_start: 0.9168 (mttt) cc_final: 0.8846 (mtpp) REVERT: F 88 TYR cc_start: 0.8954 (m-10) cc_final: 0.7992 (m-10) REVERT: G 56 GLU cc_start: 0.8623 (tt0) cc_final: 0.7986 (tt0) REVERT: G 89 ASN cc_start: 0.9236 (m-40) cc_final: 0.8752 (m-40) REVERT: G 92 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8101 (mm-30) REVERT: G 95 LYS cc_start: 0.9352 (ttpt) cc_final: 0.9101 (tttm) REVERT: H 83 TYR cc_start: 0.8147 (m-10) cc_final: 0.7505 (m-80) REVERT: K 1 MET cc_start: 0.5975 (mmt) cc_final: 0.5688 (tpp) REVERT: L 43 THR cc_start: 0.7149 (t) cc_final: 0.6741 (t) outliers start: 16 outliers final: 10 residues processed: 190 average time/residue: 0.1288 time to fit residues: 34.2070 Evaluate side-chains 186 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 176 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain K residue 147 MET Chi-restraints excluded: chain L residue 35 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 82 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 115 optimal weight: 20.0000 chunk 25 optimal weight: 0.2980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 109 HIS ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** 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 = 0.3789 r_free = 0.3789 target = 0.075003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.047468 restraints weight = 60649.344| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.78 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14225 Z= 0.149 Angle : 0.636 11.025 20458 Z= 0.366 Chirality : 0.042 0.360 2330 Planarity : 0.004 0.044 1602 Dihedral : 30.506 167.758 4180 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.37 % Allowed : 16.98 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.28), residues: 932 helix: 2.77 (0.20), residues: 631 sheet: 0.15 (0.99), residues: 24 loop : -0.17 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 139 TYR 0.017 0.001 TYR K 74 PHE 0.016 0.002 PHE L 40 TRP 0.003 0.001 TRP K 93 HIS 0.002 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (14217) covalent geometry : angle 0.62865 / 0.37 (20449) hydrogen bonds : bond 0.08219 / 5.89 ( 824) hydrogen bonds : angle 3.16365 / 2.21 ( 2006) metal coordination : bond 0.00807 / 0.53 ( 8) metal coordination : angle 4.78373 / 4.25 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8545 (mtm) cc_final: 0.8202 (mtm) REVERT: C 56 GLU cc_start: 0.8276 (tt0) cc_final: 0.7925 (tt0) REVERT: C 90 ASP cc_start: 0.8674 (t70) cc_final: 0.8369 (t70) REVERT: D 34 LYS cc_start: 0.8445 (ptpt) cc_final: 0.8102 (tptt) REVERT: D 68 ASP cc_start: 0.8931 (t70) cc_final: 0.8709 (t0) REVERT: D 108 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8562 (ttpt) REVERT: E 54 TYR cc_start: 0.9334 (m-80) cc_final: 0.8914 (m-80) REVERT: F 77 LYS cc_start: 0.9177 (mttt) cc_final: 0.8862 (mtpp) REVERT: F 88 TYR cc_start: 0.8944 (m-10) cc_final: 0.7898 (m-10) REVERT: G 56 GLU cc_start: 0.8603 (tt0) cc_final: 0.8047 (tt0) REVERT: G 89 ASN cc_start: 0.9228 (m-40) cc_final: 0.8759 (m-40) REVERT: G 92 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8083 (mm-30) REVERT: G 95 LYS cc_start: 0.9348 (ttpt) cc_final: 0.9097 (tttm) REVERT: H 83 TYR cc_start: 0.8133 (m-10) cc_final: 0.7558 (m-80) REVERT: K 1 MET cc_start: 0.5699 (mmt) cc_final: 0.5404 (tpp) REVERT: L 43 THR cc_start: 0.7066 (t) cc_final: 0.6644 (t) outliers start: 11 outliers final: 9 residues processed: 193 average time/residue: 0.1175 time to fit residues: 31.9266 Evaluate side-chains 191 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 182 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain K residue 147 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 83 optimal weight: 30.0000 chunk 99 optimal weight: 40.0000 chunk 17 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** E 113 HIS ** 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 = 0.3760 r_free = 0.3760 target = 0.073587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.045474 restraints weight = 61230.116| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.72 r_work: 0.2659 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 14225 Z= 0.275 Angle : 0.731 10.233 20458 Z= 0.404 Chirality : 0.044 0.346 2330 Planarity : 0.005 0.051 1602 Dihedral : 30.706 168.369 4180 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.50 % Allowed : 16.98 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.28), residues: 932 helix: 2.50 (0.20), residues: 633 sheet: 0.06 (0.98), residues: 24 loop : -0.23 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 79 TYR 0.021 0.002 TYR K 74 PHE 0.023 0.002 PHE L 40 TRP 0.022 0.002 TRP K 141 HIS 0.011 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.27 (14217) covalent geometry : angle 0.72254 / 0.40 (20449) hydrogen bonds : bond 0.08834 / 6.23 ( 824) hydrogen bonds : angle 3.51281 / 2.46 ( 2006) metal coordination : bond 0.01269 / 0.81 ( 8) metal coordination : angle 5.28297 / 4.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 177 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7258 (m-80) cc_final: 0.6576 (m-80) REVERT: A 42 ARG cc_start: 0.7858 (mtp85) cc_final: 0.7378 (mtp85) REVERT: A 120 MET cc_start: 0.9025 (mtm) cc_final: 0.8796 (mtm) REVERT: B 88 TYR cc_start: 0.9081 (m-10) cc_final: 0.8607 (m-10) REVERT: C 56 GLU cc_start: 0.8991 (tt0) cc_final: 0.8773 (tt0) REVERT: C 90 ASP cc_start: 0.8945 (t70) cc_final: 0.8701 (t70) REVERT: D 34 LYS cc_start: 0.8447 (ptpt) cc_final: 0.8016 (tptt) REVERT: D 68 ASP cc_start: 0.9257 (t70) cc_final: 0.9011 (t0) REVERT: D 108 LYS cc_start: 0.9248 (ttpt) cc_final: 0.9027 (ttpt) REVERT: F 77 LYS cc_start: 0.9318 (mttt) cc_final: 0.9013 (mtpp) REVERT: G 56 GLU cc_start: 0.9151 (tt0) cc_final: 0.8659 (tt0) REVERT: G 89 ASN cc_start: 0.9307 (m-40) cc_final: 0.8824 (m-40) REVERT: G 92 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8152 (mm-30) REVERT: G 95 LYS cc_start: 0.9431 (ttpt) cc_final: 0.9178 (tttm) REVERT: H 83 TYR cc_start: 0.8193 (m-10) cc_final: 0.7668 (m-80) REVERT: K 1 MET cc_start: 0.6279 (mmt) cc_final: 0.5968 (tpp) REVERT: L 43 THR cc_start: 0.7425 (OUTLIER) cc_final: 0.7041 (t) outliers start: 12 outliers final: 10 residues processed: 181 average time/residue: 0.1196 time to fit residues: 30.1269 Evaluate side-chains 186 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain K residue 147 MET Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 45 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 97 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 44 optimal weight: 0.4980 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 103 optimal weight: 8.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.074834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.046951 restraints weight = 60134.856| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.79 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14225 Z= 0.148 Angle : 0.654 10.694 20458 Z= 0.374 Chirality : 0.043 0.362 2330 Planarity : 0.004 0.061 1602 Dihedral : 30.609 168.119 4180 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.25 % Allowed : 17.73 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.28), residues: 932 helix: 2.58 (0.21), residues: 632 sheet: 0.08 (0.98), residues: 24 loop : -0.25 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 136 TYR 0.045 0.002 TYR D 83 PHE 0.025 0.002 PHE K 62 TRP 0.012 0.001 TRP K 141 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (14217) covalent geometry : angle 0.64733 / 0.37 (20449) hydrogen bonds : bond 0.08311 / 5.96 ( 824) hydrogen bonds : angle 3.21519 / 2.24 ( 2006) metal coordination : bond 0.00758 / 0.49 ( 8) metal coordination : angle 4.38760 / 3.91 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 192 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.6765 (m-80) cc_final: 0.6208 (m-80) REVERT: C 56 GLU cc_start: 0.8292 (tt0) cc_final: 0.7917 (tt0) REVERT: C 90 ASP cc_start: 0.8753 (t70) cc_final: 0.8447 (t70) REVERT: D 34 LYS cc_start: 0.8450 (ptpt) cc_final: 0.8055 (tptt) REVERT: D 68 ASP cc_start: 0.8945 (t70) cc_final: 0.8714 (t0) REVERT: D 105 GLU cc_start: 0.7650 (tp30) cc_final: 0.7437 (tp30) REVERT: D 108 LYS cc_start: 0.8812 (ttpt) cc_final: 0.8530 (ttpt) REVERT: E 54 TYR cc_start: 0.9329 (m-80) cc_final: 0.8892 (m-80) REVERT: F 77 LYS cc_start: 0.9188 (mttt) cc_final: 0.8861 (mtpp) REVERT: G 56 GLU cc_start: 0.8592 (tt0) cc_final: 0.8029 (tt0) REVERT: G 89 ASN cc_start: 0.9254 (m-40) cc_final: 0.8777 (m-40) REVERT: G 92 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8180 (mm-30) REVERT: G 95 LYS cc_start: 0.9353 (ttpt) cc_final: 0.9101 (tttm) REVERT: H 83 TYR cc_start: 0.7853 (m-10) cc_final: 0.7433 (m-80) REVERT: K 1 MET cc_start: 0.6196 (mmt) cc_final: 0.5822 (tpp) REVERT: K 62 PHE cc_start: 0.8653 (m-10) cc_final: 0.8381 (m-10) REVERT: L 43 THR cc_start: 0.6787 (t) cc_final: 0.6306 (t) outliers start: 10 outliers final: 8 residues processed: 196 average time/residue: 0.1264 time to fit residues: 34.5538 Evaluate side-chains 193 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 185 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain K residue 147 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.074120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.046132 restraints weight = 60852.346| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.77 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14225 Z= 0.209 Angle : 0.693 10.483 20458 Z= 0.388 Chirality : 0.043 0.354 2330 Planarity : 0.005 0.077 1602 Dihedral : 30.656 168.768 4180 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.12 % Allowed : 17.73 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.28), residues: 932 helix: 2.49 (0.21), residues: 631 sheet: 0.10 (0.98), residues: 24 loop : -0.29 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 136 TYR 0.071 0.003 TYR D 83 PHE 0.021 0.002 PHE K 62 TRP 0.009 0.001 TRP K 141 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.21 (14217) covalent geometry : angle 0.68229 / 0.39 (20449) hydrogen bonds : bond 0.08327 / 5.92 ( 824) hydrogen bonds : angle 3.37606 / 2.36 ( 2006) metal coordination : bond 0.00929 / 0.60 ( 8) metal coordination : angle 5.84356 / 5.56 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2789.08 seconds wall clock time: 48 minutes 29.35 seconds (2909.35 seconds total)