Starting phenix.real_space_refine on Thu Aug 6 06:50:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7k_38101/08_2026/8x7k_38101.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7k_38101/08_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_38101/08_2026/8x7k_38101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7k_38101/08_2026/8x7k_38101.map" model { file = "/net/cci-nas-00/data/ceres_data/8x7k_38101/08_2026/8x7k_38101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7k_38101/08_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-2.2rc3-6140/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: 3.33, per 1000 atoms: 0.25 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: 1.19 Conformation dependent library (CDL) restraints added in 437.1 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: 1.82 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: 2.82 Time building geometry restraints manager: 1.48 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: 18250 1.10 - 2.20: 1721 2.20 - 3.30: 438 3.30 - 4.40: 32 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.510 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.380 ------------------------------------------------------------------------------- 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= 0.529 Angle : 0.709 5.498 20458 Z= 0.621 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 0.70736 / 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 : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7277 (m-80) cc_final: 0.6724 (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: 0.7419 (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: 0.8502 (m-80) REVERT: G 56 GLU cc_start: 0.8428 (tt0) cc_final: 0.7858 (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: 0.7415 (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: 0.1640 time to fit residues: 59.3376 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 : 0.391 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.074610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.046815 restraints weight = 61207.451| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.74 r_work: 0.2701 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14225 Z= 0.199 Angle : 0.669 11.094 20458 Z= 0.385 Chirality : 0.044 0.391 2330 Planarity : 0.005 0.072 1602 Dihedral : 30.385 164.133 4186 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.75 % Allowed : 10.99 % Favored : 86.27 % 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: 2.72 (0.27), residues: 932 helix: 2.67 (0.20), residues: 626 sheet: 0.43 (1.10), residues: 22 loop : -0.10 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 55 TYR 0.026 0.002 TYR K 74 PHE 0.021 0.002 PHE K 69 TRP 0.013 0.001 TRP K 93 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.20 (14217) covalent geometry : angle 0.65527 / 0.38 (20449) hydrogen bonds : bond 0.08857 / 6.26 ( 824) hydrogen bonds : angle 3.55739 / 2.52 ( 2006) metal coordination : bond 0.02722 / 1.55 ( 8) metal coordination : angle 6.53329 / 5.79 ( 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 222 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7117 (m-80) cc_final: 0.6684 (m-80) REVERT: A 120 MET cc_start: 0.8972 (mtm) cc_final: 0.8765 (mtm) REVERT: B 22 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7382 (pp) REVERT: B 88 TYR cc_start: 0.9221 (m-10) cc_final: 0.8363 (m-10) REVERT: C 56 GLU cc_start: 0.8951 (tt0) cc_final: 0.8633 (tt0) REVERT: C 76 THR cc_start: 0.9380 (p) cc_final: 0.8973 (t) REVERT: D 34 LYS cc_start: 0.8506 (ptpt) cc_final: 0.8158 (tptt) REVERT: D 68 ASP cc_start: 0.9245 (t70) cc_final: 0.9035 (t0) REVERT: D 71 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8878 (mm-30) REVERT: D 83 TYR cc_start: 0.8200 (m-10) cc_final: 0.7781 (m-10) REVERT: D 105 GLU cc_start: 0.8575 (tp30) cc_final: 0.8155 (tp30) REVERT: E 54 TYR cc_start: 0.9444 (m-80) cc_final: 0.9153 (m-80) REVERT: F 77 LYS cc_start: 0.9240 (mttt) cc_final: 0.8933 (mtpp) REVERT: G 24 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8503 (mp10) REVERT: G 56 GLU cc_start: 0.9111 (tt0) cc_final: 0.8653 (tt0) REVERT: G 89 ASN cc_start: 0.9200 (m-40) cc_final: 0.8773 (m-40) REVERT: G 92 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8219 (mm-30) REVERT: G 95 LYS cc_start: 0.9434 (ttpt) cc_final: 0.9198 (tttm) REVERT: H 68 ASP cc_start: 0.9321 (t70) cc_final: 0.9101 (t0) REVERT: H 83 TYR cc_start: 0.7986 (m-10) cc_final: 0.7567 (m-80) REVERT: K 34 GLN cc_start: 0.8678 (tt0) cc_final: 0.8022 (tm-30) REVERT: K 46 GLN cc_start: 0.7419 (pt0) cc_final: 0.7173 (pt0) REVERT: K 74 TYR cc_start: 0.5448 (t80) cc_final: 0.5233 (t80) REVERT: K 87 ASP cc_start: 0.8785 (p0) cc_final: 0.8496 (p0) REVERT: K 117 ASP cc_start: 0.6708 (t0) cc_final: 0.6384 (p0) REVERT: K 143 GLN cc_start: 0.8843 (mt0) cc_final: 0.8603 (mp10) REVERT: L 43 THR cc_start: 0.7524 (t) cc_final: 0.7184 (t) outliers start: 22 outliers final: 15 residues processed: 209 average time/residue: 0.1155 time to fit residues: 34.1255 Evaluate side-chains 201 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 36 THR 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: 1.9990 chunk 20 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 115 optimal weight: 0.3980 chunk 77 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 101 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 47 GLN ** 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 = 0.3790 r_free = 0.3790 target = 0.075248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.047180 restraints weight = 61113.167| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.76 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 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 = 0.2920 r_free = 0.2920 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: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14225 Z= 0.150 Angle : 0.626 8.489 20458 Z= 0.368 Chirality : 0.043 0.391 2330 Planarity : 0.004 0.041 1602 Dihedral : 30.319 165.401 4182 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.12 % Allowed : 11.24 % Favored : 86.64 % 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: 2.86 (0.27), residues: 932 helix: 2.83 (0.20), residues: 625 sheet: 0.65 (1.04), residues: 22 loop : -0.19 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 72 TYR 0.021 0.002 TYR K 74 PHE 0.019 0.002 PHE K 62 TRP 0.009 0.001 TRP K 33 HIS 0.005 0.001 HIS K 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.15 (14217) covalent geometry : angle 0.61823 / 0.37 (20449) hydrogen bonds : bond 0.08357 / 5.98 ( 824) hydrogen bonds : angle 3.32022 / 2.34 ( 2006) metal coordination : bond 0.00683 / 0.45 ( 8) metal coordination : angle 4.76134 / 4.11 ( 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 226 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.6984 (m-80) cc_final: 0.6491 (m-80) REVERT: A 120 MET cc_start: 0.8540 (mtm) cc_final: 0.8224 (mtm) REVERT: C 56 GLU cc_start: 0.8332 (tt0) cc_final: 0.7935 (tt0) REVERT: C 76 THR cc_start: 0.9167 (p) cc_final: 0.8788 (t) REVERT: D 34 LYS cc_start: 0.8490 (ptpt) cc_final: 0.8151 (tptt) REVERT: D 68 ASP cc_start: 0.8954 (t70) cc_final: 0.8732 (t0) REVERT: D 71 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8224 (mm-30) REVERT: D 83 TYR cc_start: 0.7930 (m-10) cc_final: 0.7462 (m-80) REVERT: E 54 TYR cc_start: 0.9352 (m-80) cc_final: 0.9021 (m-80) REVERT: F 77 LYS cc_start: 0.9107 (mttt) cc_final: 0.8767 (mtpp) REVERT: G 24 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8465 (mp10) REVERT: G 56 GLU cc_start: 0.8609 (tt0) cc_final: 0.8086 (tt0) REVERT: G 89 ASN cc_start: 0.9195 (m-40) cc_final: 0.8755 (m-40) REVERT: G 95 LYS cc_start: 0.9344 (ttpt) cc_final: 0.9103 (tttm) REVERT: H 68 ASP cc_start: 0.9064 (t70) cc_final: 0.8795 (t0) REVERT: H 83 TYR cc_start: 0.7890 (m-10) cc_final: 0.7654 (m-80) REVERT: K 87 ASP cc_start: 0.8703 (p0) cc_final: 0.8237 (t0) REVERT: L 29 LEU cc_start: 0.7153 (mt) cc_final: 0.6896 (tp) REVERT: L 43 THR cc_start: 0.7348 (t) cc_final: 0.6874 (t) outliers start: 17 outliers final: 11 residues processed: 213 average time/residue: 0.1145 time to fit residues: 34.2841 Evaluate side-chains 199 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 188 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 95 optimal weight: 20.0000 chunk 117 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.074091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.046121 restraints weight = 60726.114| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.71 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14225 Z= 0.229 Angle : 0.686 10.272 20458 Z= 0.388 Chirality : 0.044 0.382 2330 Planarity : 0.005 0.064 1602 Dihedral : 30.437 165.821 4180 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.12 % Allowed : 13.48 % Favored : 83.40 % 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: 2.75 (0.27), residues: 932 helix: 2.74 (0.20), residues: 626 sheet: 0.62 (1.01), residues: 22 loop : -0.22 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 99 TYR 0.014 0.001 TYR K 74 PHE 0.011 0.002 PHE A 67 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 0.00467 / 0.23 (14217) covalent geometry : angle 0.67801 / 0.39 (20449) hydrogen bonds : bond 0.08577 / 6.09 ( 824) hydrogen bonds : angle 3.46612 / 2.44 ( 2006) metal coordination : bond 0.01244 / 0.79 ( 8) metal coordination : angle 4.98067 / 4.31 ( 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 214 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7026 (m-80) cc_final: 0.6533 (m-80) REVERT: A 120 MET cc_start: 0.8668 (mtm) cc_final: 0.8377 (mtm) REVERT: B 22 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7168 (pp) REVERT: B 88 TYR cc_start: 0.8915 (m-10) cc_final: 0.7706 (m-10) REVERT: C 56 GLU cc_start: 0.8388 (tt0) cc_final: 0.7995 (tt0) REVERT: D 34 LYS cc_start: 0.8503 (ptpt) cc_final: 0.8087 (tptt) REVERT: D 68 ASP cc_start: 0.8977 (t70) cc_final: 0.8731 (t0) REVERT: D 83 TYR cc_start: 0.7860 (m-10) cc_final: 0.7519 (m-10) REVERT: E 54 TYR cc_start: 0.9401 (m-80) cc_final: 0.9040 (m-80) REVERT: F 77 LYS cc_start: 0.9146 (mttt) cc_final: 0.8816 (mtpp) REVERT: G 24 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8524 (mp10) REVERT: G 56 GLU cc_start: 0.8640 (tt0) cc_final: 0.8098 (tt0) REVERT: G 89 ASN cc_start: 0.9243 (m-40) cc_final: 0.8758 (m-40) REVERT: G 95 LYS cc_start: 0.9358 (ttpt) cc_final: 0.9122 (tttm) REVERT: H 83 TYR cc_start: 0.7906 (m-10) cc_final: 0.7657 (m-80) REVERT: K 38 MET cc_start: 0.7950 (mpp) cc_final: 0.7315 (tmm) REVERT: K 87 ASP cc_start: 0.8685 (p0) cc_final: 0.8241 (t0) REVERT: K 147 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7865 (mpp) REVERT: L 43 THR cc_start: 0.7369 (t) cc_final: 0.6859 (t) outliers start: 25 outliers final: 18 residues processed: 197 average time/residue: 0.1184 time to fit residues: 32.8616 Evaluate side-chains 197 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 C residue 78 ILE Chi-restraints excluded: chain D residue 48 VAL 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 G residue 92 GLU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain K residue 143 GLN Chi-restraints excluded: chain K residue 147 MET 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: 1.9990 chunk 91 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 109 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.074753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.046907 restraints weight = 60819.954| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.71 r_work: 0.2698 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14225 Z= 0.156 Angle : 0.636 9.489 20458 Z= 0.367 Chirality : 0.043 0.390 2330 Planarity : 0.004 0.049 1602 Dihedral : 30.419 165.789 4180 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.12 % Allowed : 14.61 % Favored : 83.27 % 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: 2.84 (0.28), residues: 932 helix: 2.77 (0.21), residues: 632 sheet: 0.80 (1.09), residues: 22 loop : -0.17 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 79 TYR 0.013 0.001 TYR K 74 PHE 0.013 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 0.00287 / 0.16 (14217) covalent geometry : angle 0.62786 / 0.37 (20449) hydrogen bonds : bond 0.08304 / 5.95 ( 824) hydrogen bonds : angle 3.27985 / 2.31 ( 2006) metal coordination : bond 0.00830 / 0.56 ( 8) metal coordination : angle 4.77636 / 4.10 ( 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 212 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7239 (m-80) cc_final: 0.6863 (m-80) REVERT: A 120 MET cc_start: 0.8863 (mtm) cc_final: 0.8594 (mtm) REVERT: C 56 GLU cc_start: 0.8969 (tt0) cc_final: 0.8636 (tt0) REVERT: D 34 LYS cc_start: 0.8438 (ptpt) cc_final: 0.8015 (tptt) REVERT: D 68 ASP cc_start: 0.9219 (t70) cc_final: 0.9009 (t0) REVERT: D 83 TYR cc_start: 0.8196 (m-10) cc_final: 0.7808 (m-10) REVERT: E 50 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8915 (mt-10) REVERT: E 54 TYR cc_start: 0.9443 (m-80) cc_final: 0.9107 (m-80) REVERT: F 77 LYS cc_start: 0.9295 (mttt) cc_final: 0.8990 (mtpp) REVERT: G 24 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8572 (mp10) REVERT: G 56 GLU cc_start: 0.9140 (tt0) cc_final: 0.8687 (tt0) REVERT: G 89 ASN cc_start: 0.9300 (m-40) cc_final: 0.8831 (m-40) REVERT: G 95 LYS cc_start: 0.9407 (ttpt) cc_final: 0.9158 (tttm) REVERT: K 92 GLN cc_start: 0.8875 (tp40) cc_final: 0.8427 (mp10) REVERT: K 147 MET cc_start: 0.8379 (mtt) cc_final: 0.8162 (mpp) REVERT: L 43 THR cc_start: 0.7350 (t) cc_final: 0.6906 (t) outliers start: 17 outliers final: 13 residues processed: 200 average time/residue: 0.1104 time to fit residues: 31.4603 Evaluate side-chains 193 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 F residue 21 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 92 GLU 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: 3.9990 chunk 62 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 53 optimal weight: 30.0000 chunk 42 optimal weight: 0.5980 chunk 81 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.075217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.047283 restraints weight = 60492.110| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.81 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14225 Z= 0.139 Angle : 0.621 8.804 20458 Z= 0.361 Chirality : 0.042 0.394 2330 Planarity : 0.004 0.042 1602 Dihedral : 30.346 166.542 4180 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.12 % Allowed : 16.23 % 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: 2.89 (0.28), residues: 932 helix: 2.81 (0.21), residues: 631 sheet: 0.48 (1.05), residues: 24 loop : -0.09 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 79 TYR 0.013 0.001 TYR K 74 PHE 0.013 0.001 PHE A 67 TRP 0.005 0.001 TRP K 93 HIS 0.005 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.14 (14217) covalent geometry : angle 0.61388 / 0.36 (20449) hydrogen bonds : bond 0.08312 / 5.96 ( 824) hydrogen bonds : angle 3.15983 / 2.21 ( 2006) metal coordination : bond 0.00573 / 0.39 ( 8) metal coordination : angle 4.50385 / 3.86 ( 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: 17 poor density : 203 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.6911 (m-80) cc_final: 0.6501 (m-80) REVERT: A 120 MET cc_start: 0.8480 (mtm) cc_final: 0.8151 (mtm) REVERT: B 96 THR cc_start: 0.9321 (m) cc_final: 0.9040 (p) REVERT: C 56 GLU cc_start: 0.8260 (tt0) cc_final: 0.7916 (tt0) REVERT: D 34 LYS cc_start: 0.8462 (ptpt) cc_final: 0.8109 (tptt) REVERT: D 68 ASP cc_start: 0.8909 (t70) cc_final: 0.8692 (t0) REVERT: D 83 TYR cc_start: 0.7855 (m-10) cc_final: 0.7638 (m-10) REVERT: E 50 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8595 (mt-10) REVERT: E 54 TYR cc_start: 0.9337 (m-80) cc_final: 0.8948 (m-80) REVERT: F 22 LEU cc_start: 0.6195 (mm) cc_final: 0.5982 (mm) REVERT: F 77 LYS cc_start: 0.9160 (mttt) cc_final: 0.8835 (mtpp) REVERT: G 56 GLU cc_start: 0.8585 (tt0) cc_final: 0.8062 (tt0) REVERT: G 89 ASN cc_start: 0.9277 (m-40) cc_final: 0.8804 (m-40) REVERT: G 95 LYS cc_start: 0.9334 (ttpt) cc_final: 0.9091 (tttm) REVERT: K 1 MET cc_start: 0.5514 (mmt) cc_final: 0.5239 (tpp) REVERT: K 38 MET cc_start: 0.8439 (mpp) cc_final: 0.7775 (tmm) REVERT: K 46 GLN cc_start: 0.8808 (pp30) cc_final: 0.8538 (pm20) REVERT: K 147 MET cc_start: 0.8358 (mtt) cc_final: 0.8078 (mpp) REVERT: L 43 THR cc_start: 0.7105 (t) cc_final: 0.6653 (t) outliers start: 17 outliers final: 11 residues processed: 209 average time/residue: 0.1023 time to fit residues: 30.4191 Evaluate side-chains 198 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 187 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 F residue 21 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 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: 0.9980 chunk 79 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 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: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.074821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.046808 restraints weight = 60979.626| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.82 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14225 Z= 0.165 Angle : 0.642 10.026 20458 Z= 0.369 Chirality : 0.042 0.387 2330 Planarity : 0.004 0.055 1602 Dihedral : 30.397 167.101 4180 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.37 % Allowed : 16.23 % Favored : 81.40 % 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: 2.86 (0.28), residues: 932 helix: 2.77 (0.20), residues: 632 sheet: 0.54 (1.02), residues: 24 loop : -0.09 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 136 TYR 0.013 0.002 TYR F 88 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 0.00315 / 0.16 (14217) covalent geometry : angle 0.63408 / 0.37 (20449) hydrogen bonds : bond 0.08214 / 5.87 ( 824) hydrogen bonds : angle 3.22453 / 2.25 ( 2006) metal coordination : bond 0.00828 / 0.54 ( 8) metal coordination : angle 4.72149 / 4.12 ( 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 209 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.6882 (m-80) cc_final: 0.6438 (m-80) REVERT: A 73 GLU cc_start: 0.8311 (tt0) cc_final: 0.7987 (tt0) REVERT: A 120 MET cc_start: 0.8523 (mtm) cc_final: 0.8201 (mtm) REVERT: B 96 THR cc_start: 0.9356 (m) cc_final: 0.9058 (p) REVERT: C 56 GLU cc_start: 0.8278 (tt0) cc_final: 0.7931 (tt0) REVERT: D 34 LYS cc_start: 0.8461 (ptpt) cc_final: 0.8055 (tptt) REVERT: D 68 ASP cc_start: 0.8943 (t70) cc_final: 0.8720 (t0) REVERT: D 83 TYR cc_start: 0.7794 (m-10) cc_final: 0.7553 (m-10) REVERT: E 54 TYR cc_start: 0.9345 (m-80) cc_final: 0.8933 (m-80) REVERT: F 77 LYS cc_start: 0.9164 (mttt) cc_final: 0.8849 (mtpp) REVERT: G 56 GLU cc_start: 0.8624 (tt0) cc_final: 0.7989 (tt0) REVERT: G 89 ASN cc_start: 0.9285 (m-40) cc_final: 0.8784 (m-40) REVERT: G 95 LYS cc_start: 0.9338 (ttpt) cc_final: 0.9095 (tttm) REVERT: H 83 TYR cc_start: 0.7999 (m-10) cc_final: 0.7505 (m-80) REVERT: K 1 MET cc_start: 0.5990 (mmt) cc_final: 0.5692 (tpp) REVERT: K 45 TYR cc_start: 0.5421 (m-80) cc_final: 0.5129 (m-80) REVERT: K 46 GLN cc_start: 0.8766 (pp30) cc_final: 0.8497 (pm20) REVERT: K 147 MET cc_start: 0.8336 (mtt) cc_final: 0.8104 (mpp) REVERT: L 43 THR cc_start: 0.7050 (t) cc_final: 0.6637 (t) outliers start: 19 outliers final: 14 residues processed: 199 average time/residue: 0.1338 time to fit residues: 37.2928 Evaluate side-chains 197 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 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 D residue 90 THR 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 92 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR 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: 6.9990 chunk 80 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.074884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.047337 restraints weight = 60917.256| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.71 r_work: 0.2706 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14225 Z= 0.165 Angle : 0.648 9.553 20458 Z= 0.370 Chirality : 0.043 0.388 2330 Planarity : 0.004 0.074 1602 Dihedral : 30.435 167.479 4180 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.50 % Allowed : 17.48 % 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: 2.81 (0.27), residues: 932 helix: 2.76 (0.20), residues: 632 sheet: 0.55 (1.01), residues: 24 loop : -0.18 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 136 TYR 0.016 0.001 TYR F 88 PHE 0.021 0.002 PHE L 40 TRP 0.003 0.001 TRP K 93 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (14217) covalent geometry : angle 0.64244 / 0.37 (20449) hydrogen bonds : bond 0.08178 / 5.85 ( 824) hydrogen bonds : angle 3.19936 / 2.23 ( 2006) metal coordination : bond 0.00845 / 0.56 ( 8) metal coordination : angle 4.10168 / 3.62 ( 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 203 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 191 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8903 (mtm) cc_final: 0.8624 (mtm) REVERT: C 56 GLU cc_start: 0.8953 (tt0) cc_final: 0.8633 (tt0) REVERT: D 34 LYS cc_start: 0.8428 (ptpt) cc_final: 0.8056 (tptt) REVERT: D 68 ASP cc_start: 0.9216 (t70) cc_final: 0.8966 (t0) REVERT: F 77 LYS cc_start: 0.9318 (mttt) cc_final: 0.9032 (mtpp) REVERT: G 56 GLU cc_start: 0.9149 (tt0) cc_final: 0.8665 (tt0) REVERT: G 89 ASN cc_start: 0.9291 (m-40) cc_final: 0.8819 (m-40) REVERT: G 95 LYS cc_start: 0.9397 (ttpt) cc_final: 0.9144 (tttm) REVERT: H 83 TYR cc_start: 0.8079 (m-10) cc_final: 0.7712 (m-80) REVERT: K 1 MET cc_start: 0.6104 (mmt) cc_final: 0.5780 (tpp) REVERT: K 38 MET cc_start: 0.8320 (mpp) cc_final: 0.7784 (tmm) REVERT: K 45 TYR cc_start: 0.5689 (m-80) cc_final: 0.5376 (m-80) REVERT: K 46 GLN cc_start: 0.8782 (pp30) cc_final: 0.8558 (pm20) REVERT: K 147 MET cc_start: 0.8394 (mtt) cc_final: 0.8184 (mpp) REVERT: L 41 GLN cc_start: 0.7722 (mt0) cc_final: 0.7467 (pt0) REVERT: L 43 THR cc_start: 0.7205 (t) cc_final: 0.6790 (t) outliers start: 12 outliers final: 11 residues processed: 196 average time/residue: 0.1289 time to fit residues: 35.4271 Evaluate side-chains 197 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 186 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 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 G residue 92 GLU Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 27 optimal weight: 3.9990 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: 5.9990 chunk 80 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.073820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.045714 restraints weight = 60962.260| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.71 r_work: 0.2666 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14225 Z= 0.244 Angle : 0.705 9.268 20458 Z= 0.393 Chirality : 0.044 0.380 2330 Planarity : 0.005 0.055 1602 Dihedral : 30.600 168.021 4180 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.75 % Allowed : 17.10 % 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: 2.58 (0.28), residues: 932 helix: 2.55 (0.20), residues: 633 sheet: 0.60 (1.01), residues: 24 loop : -0.21 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 136 TYR 0.021 0.002 TYR F 88 PHE 0.011 0.002 PHE L 40 TRP 0.004 0.001 TRP K 93 HIS 0.009 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.24 (14217) covalent geometry : angle 0.69858 / 0.39 (20449) hydrogen bonds : bond 0.08564 / 6.06 ( 824) hydrogen bonds : angle 3.42301 / 2.39 ( 2006) metal coordination : bond 0.01034 / 0.67 ( 8) metal coordination : angle 4.49298 / 4.09 ( 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 194 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8987 (mtm) cc_final: 0.8746 (mtm) REVERT: B 88 TYR cc_start: 0.9054 (m-10) cc_final: 0.8644 (m-10) REVERT: C 56 GLU cc_start: 0.8977 (tt0) cc_final: 0.8651 (tt0) REVERT: D 34 LYS cc_start: 0.8453 (ptpt) cc_final: 0.8016 (tptt) REVERT: D 68 ASP cc_start: 0.9242 (t70) cc_final: 0.9004 (t0) REVERT: F 77 LYS cc_start: 0.9335 (mttt) cc_final: 0.9040 (mtpp) REVERT: G 56 GLU cc_start: 0.9147 (tt0) cc_final: 0.8649 (tt0) REVERT: G 89 ASN cc_start: 0.9321 (m-40) cc_final: 0.8828 (m-40) REVERT: G 95 LYS cc_start: 0.9406 (ttpt) cc_final: 0.9162 (tttm) REVERT: H 83 TYR cc_start: 0.8092 (m-10) cc_final: 0.7722 (m-80) REVERT: K 1 MET cc_start: 0.6262 (mmt) cc_final: 0.5938 (tpp) REVERT: K 45 TYR cc_start: 0.5826 (m-80) cc_final: 0.5435 (m-80) REVERT: K 46 GLN cc_start: 0.8798 (pp30) cc_final: 0.8565 (pm20) REVERT: K 147 MET cc_start: 0.8409 (mtt) cc_final: 0.8208 (mpp) REVERT: L 41 GLN cc_start: 0.7653 (mt0) cc_final: 0.7324 (pt0) REVERT: L 43 THR cc_start: 0.7558 (t) cc_final: 0.7154 (t) outliers start: 14 outliers final: 12 residues processed: 185 average time/residue: 0.1328 time to fit residues: 34.4849 Evaluate side-chains 188 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 E residue 68 GLN Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 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: 30.0000 chunk 44 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.0470 chunk 37 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 117 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 103 optimal weight: 20.0000 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.075113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.047303 restraints weight = 59947.933| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.78 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2666 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= 0.141 Angle : 0.653 9.638 20458 Z= 0.373 Chirality : 0.043 0.397 2330 Planarity : 0.004 0.048 1602 Dihedral : 30.455 168.093 4180 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.25 % Allowed : 18.23 % Favored : 80.52 % 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: 2.65 (0.28), residues: 932 helix: 2.61 (0.21), residues: 632 sheet: 0.78 (1.04), residues: 24 loop : -0.20 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 136 TYR 0.040 0.002 TYR D 83 PHE 0.023 0.001 PHE K 62 TRP 0.003 0.000 TRP K 141 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (14217) covalent geometry : angle 0.64757 / 0.37 (20449) hydrogen bonds : bond 0.08373 / 6.01 ( 824) hydrogen bonds : angle 3.17178 / 2.21 ( 2006) metal coordination : bond 0.00651 / 0.40 ( 8) metal coordination : angle 4.01224 / 3.65 ( 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 204 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 194 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8165 (mtp85) cc_final: 0.7912 (mtp-110) REVERT: C 56 GLU cc_start: 0.8303 (tt0) cc_final: 0.7918 (tt0) REVERT: D 34 LYS cc_start: 0.8471 (ptpt) cc_final: 0.8065 (tptt) REVERT: D 68 ASP cc_start: 0.8944 (t70) cc_final: 0.8716 (t0) REVERT: E 54 TYR cc_start: 0.9331 (m-80) cc_final: 0.8902 (m-80) REVERT: F 77 LYS cc_start: 0.9195 (mttt) cc_final: 0.8875 (mtpp) REVERT: G 56 GLU cc_start: 0.8607 (tt0) cc_final: 0.8033 (tt0) REVERT: G 89 ASN cc_start: 0.9277 (m-40) cc_final: 0.8763 (m-40) REVERT: G 95 LYS cc_start: 0.9338 (ttpt) cc_final: 0.9086 (tttm) REVERT: H 83 TYR cc_start: 0.7827 (m-10) cc_final: 0.7429 (m-10) REVERT: K 1 MET cc_start: 0.6101 (mmt) cc_final: 0.5785 (tpp) REVERT: K 45 TYR cc_start: 0.5337 (m-80) cc_final: 0.4984 (m-80) REVERT: K 62 PHE cc_start: 0.8637 (m-10) cc_final: 0.8352 (m-10) REVERT: L 41 GLN cc_start: 0.7606 (mt0) cc_final: 0.7284 (pt0) REVERT: L 43 THR cc_start: 0.6809 (t) cc_final: 0.6339 (t) outliers start: 10 outliers final: 8 residues processed: 199 average time/residue: 0.1142 time to fit residues: 31.9632 Evaluate side-chains 198 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 190 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 62 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain L residue 40 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** 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 = 0.3768 r_free = 0.3768 target = 0.073904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.045891 restraints weight = 60785.395| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.70 r_work: 0.2674 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14225 Z= 0.235 Angle : 0.711 10.694 20458 Z= 0.393 Chirality : 0.044 0.381 2330 Planarity : 0.005 0.066 1602 Dihedral : 30.560 168.761 4180 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.25 % Allowed : 18.10 % Favored : 80.65 % 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: 2.50 (0.28), residues: 932 helix: 2.48 (0.20), residues: 632 sheet: 0.57 (1.03), residues: 24 loop : -0.23 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 79 TYR 0.064 0.003 TYR D 83 PHE 0.021 0.002 PHE K 62 TRP 0.020 0.002 TRP K 141 HIS 0.005 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.23 (14217) covalent geometry : angle 0.70202 / 0.39 (20449) hydrogen bonds : bond 0.08460 / 5.99 ( 824) hydrogen bonds : angle 3.37766 / 2.35 ( 2006) metal coordination : bond 0.00931 / 0.59 ( 8) metal coordination : angle 5.28507 / 5.09 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2967.68 seconds wall clock time: 51 minutes 24.40 seconds (3084.40 seconds total)