Starting phenix.real_space_refine on Thu Aug 6 12:39:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8grq_34212/08_2026/8grq_34212.cif Found real_map, /net/cci-nas-00/data/ceres_data/8grq_34212/08_2026/8grq_34212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8grq_34212/08_2026/8grq_34212.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8grq_34212/08_2026/8grq_34212.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8grq_34212/08_2026/8grq_34212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8grq_34212/08_2026/8grq_34212.map" model { file = "/net/cci-nas-00/data/ceres_data/8grq_34212/08_2026/8grq_34212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8grq_34212/08_2026/8grq_34212.cif" } resolution = 3.87 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 1168 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 4 6.06 5 P 294 5.49 5 S 36 5.16 5 C 8230 2.51 5 N 2706 2.21 5 O 3293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 14563 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" 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: "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: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} 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: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 722 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 87} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 602 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 80} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "N" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1174 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "K" 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} Chain: "M" 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 12208 SG CYS K 24 62.105 63.367 34.776 1.00172.74 S ATOM 12229 SG CYS K 27 58.255 63.031 33.350 1.00177.83 S ATOM 12365 SG CYS K 44 59.781 65.988 34.198 1.00172.35 S ATOM 12391 SG CYS K 47 58.931 63.740 37.112 1.00176.07 S ATOM 12322 SG CYS K 39 70.895 59.640 45.120 1.00151.18 S ATOM 12495 SG CYS K 61 67.586 57.821 45.169 1.00176.74 S ATOM 12513 SG CYS K 64 70.913 55.890 45.707 1.00187.38 S ATOM 12906 SG CYS M 50 87.356 78.652 40.369 1.00315.19 S ATOM 12929 SG CYS M 53 91.231 78.160 41.005 1.00349.31 S ATOM 13066 SG CYS M 71 88.943 75.205 40.394 1.00330.74 S ATOM 13086 SG CYS M 74 88.955 77.314 43.618 1.00335.17 S ATOM 13022 SG CYS M 66 77.403 77.457 48.921 1.00288.65 S ATOM 13142 SG CYS M 83 79.789 79.735 50.921 1.00333.44 S ATOM 13162 SG CYS M 86 76.503 81.265 49.555 1.00326.82 S Time building chain proxies: 2.97, per 1000 atoms: 0.20 Number of scatterers: 14563 At special positions: 0 Unit cell: (120.288, 124.584, 121.362, 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 4 29.99 S 36 16.00 P 294 15.00 O 3293 8.00 N 2706 7.00 C 8230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 354.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 101 " pdb="ZN ZN K 101 " - pdb=" SG CYS K 44 " pdb="ZN ZN K 101 " - pdb=" SG CYS K 27 " pdb="ZN ZN K 101 " - pdb=" SG CYS K 47 " pdb="ZN ZN K 101 " - pdb=" SG CYS K 24 " pdb=" ZN K 102 " pdb="ZN ZN K 102 " - pdb=" NE2 HIS K 41 " pdb="ZN ZN K 102 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 102 " - pdb=" SG CYS K 61 " pdb="ZN ZN K 102 " - pdb=" SG CYS K 64 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 74 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 53 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 71 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 50 " pdb=" ZN M 202 " pdb="ZN ZN M 202 " - pdb=" ND1 HIS M 68 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 83 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 86 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 66 " Number of angles added : 18 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2046 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 12 sheets defined 63.5% alpha, 3.9% beta 145 base pairs and 241 stacking pairs defined. Time for finding SS restraints: 1.96 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 132 removed outlier: 3.692A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.609A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.596A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.368A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.636A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) 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 removed outlier: 3.761A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.585A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.727A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.569A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.657A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.667A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.650A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.818A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.321A 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 7 through 22 Processing helix chain 'K' and resid 46 through 54 Processing helix chain 'K' and resid 79 through 97 removed outlier: 4.404A pdb=" N GLU K 84 " --> pdb=" O SER K 80 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU K 85 " --> pdb=" O GLN K 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 49 removed outlier: 4.329A pdb=" N ALA M 39 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 77 removed outlier: 3.532A pdb=" N VAL M 75 " --> pdb=" O CYS M 71 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASP M 77 " --> pdb=" O ASN M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 116 Processing helix chain 'N' and resid 2 through 16 removed outlier: 3.743A pdb=" N LEU N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 90 Processing helix chain 'N' and resid 98 through 112 removed outlier: 3.537A pdb=" N LEU N 104 " --> pdb=" O SER N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 130 Processing helix chain 'N' and resid 130 through 146 removed outlier: 3.501A pdb=" N TYR N 134 " --> pdb=" O ASP N 130 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.889A 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: 7.963A 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 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.941A 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 removed outlier: 3.533A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.705A 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 35 through 36 removed outlier: 3.725A pdb=" N VAL K 35 " --> pdb=" O PHE K 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 22 through 25 501 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 371 hydrogen bonds 738 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 241 stacking parallelities Total time for adding SS restraints: 2.55 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3605 1.34 - 1.46: 4658 1.46 - 1.58: 6518 1.58 - 1.70: 586 1.70 - 1.82: 53 Bond restraints: 15420 Sorted by residual: bond pdb=" C3' DA I -53 " pdb=" C2' DA I -53 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DA J -67 " pdb=" C2' DA J -67 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DC I -11 " pdb=" C2' DC I -11 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DG I 62 " pdb=" C2' DG I 62 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DG I 21 " pdb=" C2' DG I 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 15415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 21116 1.86 - 3.72: 916 3.72 - 5.59: 48 5.59 - 7.45: 13 7.45 - 9.31: 3 Bond angle restraints: 22096 Sorted by residual: angle pdb=" O4' DA I 47 " pdb=" C4' DA I 47 " pdb=" C3' DA I 47 " ideal model delta sigma weight residual 106.00 102.85 3.15 6.00e-01 2.78e+00 2.75e+01 angle pdb=" N3 DT J 30 " pdb=" C4 DT J 30 " pdb=" O4 DT J 30 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT J -42 " pdb=" C4 DT J -42 " pdb=" O4 DT J -42 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT J 71 " pdb=" C4 DT J 71 " pdb=" O4 DT J 71 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT I 66 " pdb=" C4 DT I 66 " pdb=" O4 DT I 66 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 ... (remaining 22091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.16: 7210 34.16 - 68.31: 1338 68.31 - 102.47: 20 102.47 - 136.63: 2 136.63 - 170.79: 2 Dihedral angle restraints: 8572 sinusoidal: 5417 harmonic: 3155 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 220.00 49.21 170.79 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA GLU A 50 " pdb=" C GLU A 50 " pdb=" N ILE A 51 " pdb=" CA ILE A 51 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+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 69.51 150.49 1 3.50e+01 8.16e-04 1.47e+01 ... (remaining 8569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1538 0.037 - 0.073: 661 0.073 - 0.110: 269 0.110 - 0.147: 45 0.147 - 0.184: 6 Chirality restraints: 2519 Sorted by residual: chirality pdb=" C3' DT I 15 " pdb=" C4' DT I 15 " pdb=" O3' DT I 15 " pdb=" C2' DT I 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.43e-01 chirality pdb=" CA GLU F 63 " pdb=" N GLU F 63 " pdb=" C GLU F 63 " pdb=" CB GLU F 63 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.31e-01 chirality pdb=" CA GLU B 63 " pdb=" N GLU B 63 " pdb=" C GLU B 63 " pdb=" CB GLU B 63 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.02e-01 ... (remaining 2516 not shown) Planarity restraints: 1788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 109 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C LEU A 109 " 0.031 2.00e-02 2.50e+03 pdb=" O LEU A 109 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A 110 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS K 45 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C LYS K 45 " 0.031 2.00e-02 2.50e+03 pdb=" O LYS K 45 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE K 46 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE K 46 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C PHE K 46 " -0.029 2.00e-02 2.50e+03 pdb=" O PHE K 46 " 0.011 2.00e-02 2.50e+03 pdb=" N CYS K 47 " 0.010 2.00e-02 2.50e+03 ... (remaining 1785 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 512 2.68 - 3.24: 13853 3.24 - 3.79: 28007 3.79 - 4.35: 34420 4.35 - 4.90: 49151 Nonbonded interactions: 125943 Sorted by model distance: nonbonded pdb=" N2 DG I -10 " pdb=" O2 DC J 10 " model vdw 2.125 2.496 nonbonded pdb=" O GLN M 106 " pdb=" OG SER M 109 " model vdw 2.199 3.040 nonbonded pdb=" NH1 ARG F 92 " pdb=" OE2 GLU H 76 " model vdw 2.205 3.120 nonbonded pdb=" OH TYR C 57 " pdb=" NH1 ARG K 71 " model vdw 2.209 3.120 nonbonded pdb=" O ARG N 139 " pdb=" OG1 THR N 142 " model vdw 2.210 3.040 ... (remaining 125938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 10 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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 group one per residue 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 15.950 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 0.112 15436 Z= 0.475 Angle : 0.814 14.367 22114 Z= 0.647 Chirality : 0.047 0.184 2519 Planarity : 0.004 0.040 1788 Dihedral : 25.399 170.786 6526 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.22 % Allowed : 0.33 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.25), residues: 1062 helix: 1.19 (0.21), residues: 656 sheet: 0.77 (1.20), residues: 18 loop : -0.87 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 95 TYR 0.020 0.002 TYR B 88 PHE 0.013 0.001 PHE K 79 TRP 0.008 0.001 TRP N 93 HIS 0.005 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.47 (15420) covalent geometry : angle 0.79430 / 0.65 (22096) hydrogen bonds : bond 0.14169 / 9.23 ( 872) hydrogen bonds : angle 5.32690 / 3.83 ( 2220) metal coordination : bond 0.03062 / 1.56 ( 16) metal coordination : angle 6.26842 / 3.15 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 527 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9766 (mp) cc_final: 0.9175 (mp) REVERT: A 70 LEU cc_start: 0.9664 (tp) cc_final: 0.9309 (tt) REVERT: A 99 TYR cc_start: 0.9195 (t80) cc_final: 0.8919 (t80) REVERT: A 108 ASN cc_start: 0.9285 (t0) cc_final: 0.8989 (t0) REVERT: A 112 ILE cc_start: 0.9420 (pt) cc_final: 0.9082 (mt) REVERT: A 120 MET cc_start: 0.8940 (mmm) cc_final: 0.8638 (mmm) REVERT: B 24 ASP cc_start: 0.7033 (t0) cc_final: 0.6811 (t0) REVERT: B 29 ILE cc_start: 0.9564 (mm) cc_final: 0.9316 (mp) REVERT: B 34 ILE cc_start: 0.9766 (mt) cc_final: 0.9554 (mm) REVERT: B 45 ARG cc_start: 0.8887 (ttt180) cc_final: 0.8457 (ttt-90) REVERT: B 49 LEU cc_start: 0.9020 (mm) cc_final: 0.8594 (mt) REVERT: B 53 GLU cc_start: 0.8288 (pm20) cc_final: 0.7655 (pm20) REVERT: B 79 LYS cc_start: 0.9163 (mtmt) cc_final: 0.8860 (ptpt) REVERT: C 38 ASN cc_start: 0.8806 (m-40) cc_final: 0.8502 (p0) REVERT: C 68 ASN cc_start: 0.9307 (m-40) cc_final: 0.8787 (m110) REVERT: C 100 VAL cc_start: 0.9689 (m) cc_final: 0.9467 (t) REVERT: C 101 THR cc_start: 0.9167 (m) cc_final: 0.8763 (p) REVERT: D 59 MET cc_start: 0.9381 (tpp) cc_final: 0.9075 (tpt) REVERT: D 68 ASP cc_start: 0.9103 (t0) cc_final: 0.8706 (t0) REVERT: D 88 THR cc_start: 0.9310 (m) cc_final: 0.9091 (p) REVERT: D 101 LEU cc_start: 0.9583 (mt) cc_final: 0.9303 (mp) REVERT: E 48 LEU cc_start: 0.9695 (mt) cc_final: 0.9267 (mm) REVERT: E 50 GLU cc_start: 0.9062 (pt0) cc_final: 0.8524 (pt0) REVERT: E 60 LEU cc_start: 0.9103 (mt) cc_final: 0.8154 (mt) REVERT: E 97 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8286 (mt-10) REVERT: E 108 ASN cc_start: 0.9331 (t0) cc_final: 0.9102 (t0) REVERT: E 112 ILE cc_start: 0.9026 (mp) cc_final: 0.8810 (mp) REVERT: E 119 ILE cc_start: 0.9494 (mm) cc_final: 0.9048 (mm) REVERT: F 35 ARG cc_start: 0.9221 (mtp-110) cc_final: 0.8994 (ttm-80) REVERT: F 39 ARG cc_start: 0.9116 (mmt90) cc_final: 0.8396 (mmt90) REVERT: F 44 LYS cc_start: 0.9291 (tptm) cc_final: 0.8916 (tttm) REVERT: F 49 LEU cc_start: 0.9349 (mt) cc_final: 0.8978 (mt) REVERT: F 78 ARG cc_start: 0.8568 (mtm110) cc_final: 0.8339 (mtm-85) REVERT: F 82 THR cc_start: 0.8895 (p) cc_final: 0.8679 (t) REVERT: F 88 TYR cc_start: 0.8981 (m-10) cc_final: 0.8422 (m-10) REVERT: G 32 ARG cc_start: 0.9137 (ttp80) cc_final: 0.8772 (ttp80) REVERT: G 35 ARG cc_start: 0.8344 (mtm110) cc_final: 0.7456 (ptm-80) REVERT: G 36 LYS cc_start: 0.8588 (mmtm) cc_final: 0.7752 (mmtm) REVERT: G 38 ASN cc_start: 0.9048 (m-40) cc_final: 0.8830 (m-40) REVERT: G 39 TYR cc_start: 0.9372 (m-80) cc_final: 0.9033 (m-80) REVERT: G 75 LYS cc_start: 0.9335 (mttm) cc_final: 0.8898 (mmmm) REVERT: H 68 ASP cc_start: 0.9155 (t0) cc_final: 0.8951 (t0) REVERT: H 70 PHE cc_start: 0.9371 (t80) cc_final: 0.8935 (t80) REVERT: H 83 TYR cc_start: 0.8666 (m-10) cc_final: 0.8355 (m-10) REVERT: H 101 LEU cc_start: 0.9258 (mp) cc_final: 0.8837 (mp) REVERT: H 105 GLU cc_start: 0.8289 (tp30) cc_final: 0.7945 (tp30) REVERT: N 38 MET cc_start: 0.3018 (ppp) cc_final: 0.2749 (ppp) REVERT: N 79 ASN cc_start: 0.6534 (p0) cc_final: 0.6268 (p0) outliers start: 2 outliers final: 1 residues processed: 529 average time/residue: 0.1514 time to fit residues: 108.8203 Evaluate side-chains 414 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 413 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN D 109 HIS E 68 GLN G 31 HIS G 68 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 143 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.050774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.040494 restraints weight = 94137.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.041718 restraints weight = 44757.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.042522 restraints weight = 27111.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.043094 restraints weight = 19182.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.043499 restraints weight = 15104.677| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 15436 Z= 0.289 Angle : 0.852 16.778 22114 Z= 0.465 Chirality : 0.049 0.295 2519 Planarity : 0.006 0.047 1788 Dihedral : 29.338 170.823 4404 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.26 % Allowed : 19.93 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.25), residues: 1062 helix: 0.78 (0.19), residues: 669 sheet: 0.54 (1.20), residues: 24 loop : -0.95 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 33 TYR 0.042 0.003 TYR D 83 PHE 0.028 0.002 PHE F 61 TRP 0.010 0.001 TRP N 141 HIS 0.011 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.29 (15420) covalent geometry : angle 0.82044 / 0.46 (22096) hydrogen bonds : bond 0.06772 / 4.54 ( 872) hydrogen bonds : angle 4.26672 / 3.04 ( 2220) metal coordination : bond 0.02345 / 1.31 ( 16) metal coordination : angle 8.15813 / 4.36 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 439 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9559 (t80) cc_final: 0.9307 (t80) REVERT: A 80 THR cc_start: 0.9374 (OUTLIER) cc_final: 0.9156 (p) REVERT: A 85 GLN cc_start: 0.8903 (mt0) cc_final: 0.8462 (mt0) REVERT: A 93 GLN cc_start: 0.8906 (tp40) cc_final: 0.8629 (tp40) REVERT: A 94 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8936 (mm-30) REVERT: A 105 GLU cc_start: 0.9011 (tp30) cc_final: 0.8654 (tp30) REVERT: A 112 ILE cc_start: 0.9459 (pt) cc_final: 0.9164 (mt) REVERT: A 120 MET cc_start: 0.8860 (mmm) cc_final: 0.8532 (mtp) REVERT: B 24 ASP cc_start: 0.7590 (t0) cc_final: 0.7369 (t0) REVERT: B 49 LEU cc_start: 0.8959 (mm) cc_final: 0.8526 (mt) REVERT: B 52 GLU cc_start: 0.8142 (pm20) cc_final: 0.7486 (pm20) REVERT: B 53 GLU cc_start: 0.7968 (pm20) cc_final: 0.7719 (pm20) REVERT: B 79 LYS cc_start: 0.9130 (mtmt) cc_final: 0.8797 (ptpt) REVERT: C 23 LEU cc_start: 0.9140 (mt) cc_final: 0.8931 (mt) REVERT: C 38 ASN cc_start: 0.9054 (m-40) cc_final: 0.8615 (p0) REVERT: C 68 ASN cc_start: 0.9346 (m-40) cc_final: 0.9109 (m110) REVERT: C 101 THR cc_start: 0.9186 (m) cc_final: 0.8702 (p) REVERT: D 68 ASP cc_start: 0.9305 (t0) cc_final: 0.9032 (t0) REVERT: D 88 THR cc_start: 0.9516 (m) cc_final: 0.9212 (p) REVERT: D 96 THR cc_start: 0.9578 (m) cc_final: 0.9336 (p) REVERT: E 50 GLU cc_start: 0.9377 (pt0) cc_final: 0.8578 (pt0) REVERT: E 122 LYS cc_start: 0.9183 (ptmt) cc_final: 0.8916 (ptmt) REVERT: E 125 GLN cc_start: 0.9425 (mt0) cc_final: 0.9007 (mp10) REVERT: F 35 ARG cc_start: 0.9383 (mtp-110) cc_final: 0.9140 (ttm-80) REVERT: F 39 ARG cc_start: 0.9245 (mmt90) cc_final: 0.8373 (mmt90) REVERT: F 49 LEU cc_start: 0.9283 (mt) cc_final: 0.8995 (mm) REVERT: F 51 TYR cc_start: 0.8880 (m-80) cc_final: 0.8540 (m-80) REVERT: F 79 LYS cc_start: 0.9205 (mtpp) cc_final: 0.8836 (mtmm) REVERT: F 84 MET cc_start: 0.8868 (mmm) cc_final: 0.8599 (mmm) REVERT: F 88 TYR cc_start: 0.9308 (m-10) cc_final: 0.8979 (m-80) REVERT: F 95 ARG cc_start: 0.8951 (mtp85) cc_final: 0.8714 (mtt90) REVERT: G 32 ARG cc_start: 0.9277 (ttp80) cc_final: 0.8964 (ttp80) REVERT: G 36 LYS cc_start: 0.8575 (mmtm) cc_final: 0.8319 (mmtm) REVERT: G 38 ASN cc_start: 0.9308 (m-40) cc_final: 0.9062 (m-40) REVERT: G 39 TYR cc_start: 0.9493 (m-80) cc_final: 0.9274 (m-80) REVERT: G 75 LYS cc_start: 0.9372 (mttm) cc_final: 0.9120 (mmmm) REVERT: H 37 TYR cc_start: 0.9438 (m-80) cc_final: 0.9227 (m-80) REVERT: H 42 TYR cc_start: 0.8779 (t80) cc_final: 0.8553 (t80) REVERT: H 72 ARG cc_start: 0.9344 (ttm170) cc_final: 0.9142 (ttm170) REVERT: H 84 ASN cc_start: 0.9373 (m110) cc_final: 0.9161 (m110) REVERT: H 92 ARG cc_start: 0.8828 (mtp-110) cc_final: 0.8297 (ttp80) REVERT: H 106 LEU cc_start: 0.9304 (mt) cc_final: 0.8999 (mt) REVERT: K 50 LYS cc_start: 0.9238 (mptt) cc_final: 0.8953 (mmtm) REVERT: M 77 ASP cc_start: 0.8252 (m-30) cc_final: 0.7548 (p0) REVERT: M 104 MET cc_start: 0.8935 (mmm) cc_final: 0.8543 (mmt) REVERT: N 38 MET cc_start: 0.3114 (ppp) cc_final: 0.2824 (ppp) REVERT: N 56 PHE cc_start: 0.8222 (m-80) cc_final: 0.7717 (m-80) REVERT: N 79 ASN cc_start: 0.6279 (p0) cc_final: 0.5945 (p0) outliers start: 48 outliers final: 32 residues processed: 455 average time/residue: 0.1198 time to fit residues: 75.7230 Evaluate side-chains 436 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 403 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain N residue 84 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 86 optimal weight: 30.0000 chunk 107 optimal weight: 10.0000 chunk 27 optimal weight: 0.0370 chunk 4 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 37 optimal weight: 0.0770 chunk 45 optimal weight: 0.0870 chunk 24 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN C 82 HIS ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN H 109 HIS ** K 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.052609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.041951 restraints weight = 92651.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.043253 restraints weight = 42446.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.044122 restraints weight = 25253.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.044749 restraints weight = 17576.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.045228 restraints weight = 13774.409| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 15436 Z= 0.167 Angle : 0.758 14.009 22114 Z= 0.413 Chirality : 0.046 0.379 2519 Planarity : 0.005 0.048 1788 Dihedral : 29.492 171.733 4404 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.18 % Allowed : 23.66 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.25), residues: 1062 helix: 0.94 (0.20), residues: 661 sheet: 0.44 (1.17), residues: 24 loop : -0.92 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 112 TYR 0.033 0.002 TYR D 83 PHE 0.034 0.002 PHE E 67 TRP 0.008 0.001 TRP N 141 HIS 0.010 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.17 (15420) covalent geometry : angle 0.73037 / 0.41 (22096) hydrogen bonds : bond 0.04897 / 3.30 ( 872) hydrogen bonds : angle 3.82875 / 2.72 ( 2220) metal coordination : bond 0.02862 / 1.45 ( 16) metal coordination : angle 7.19719 / 3.78 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 460 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8782 (tptt) cc_final: 0.8352 (tttm) REVERT: A 80 THR cc_start: 0.9419 (OUTLIER) cc_final: 0.9038 (m) REVERT: A 85 GLN cc_start: 0.8728 (mt0) cc_final: 0.8345 (mt0) REVERT: A 93 GLN cc_start: 0.8871 (tp40) cc_final: 0.8338 (tp40) REVERT: A 105 GLU cc_start: 0.9019 (tp30) cc_final: 0.8586 (tp30) REVERT: A 112 ILE cc_start: 0.9319 (pt) cc_final: 0.9093 (mt) REVERT: A 129 ARG cc_start: 0.8755 (tpm170) cc_final: 0.8532 (tpm170) REVERT: B 35 ARG cc_start: 0.8962 (mtm-85) cc_final: 0.8581 (ttm110) REVERT: B 49 LEU cc_start: 0.8923 (mm) cc_final: 0.8489 (tp) REVERT: B 52 GLU cc_start: 0.8188 (pm20) cc_final: 0.7655 (pm20) REVERT: B 79 LYS cc_start: 0.9074 (mtmt) cc_final: 0.8677 (ptpt) REVERT: C 38 ASN cc_start: 0.8959 (m-40) cc_final: 0.8547 (p0) REVERT: C 68 ASN cc_start: 0.9405 (m-40) cc_final: 0.9199 (m110) REVERT: C 101 THR cc_start: 0.9081 (m) cc_final: 0.8602 (p) REVERT: D 68 ASP cc_start: 0.9331 (t0) cc_final: 0.8976 (t0) REVERT: D 71 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8752 (tm-30) REVERT: D 79 ARG cc_start: 0.9262 (ttp-110) cc_final: 0.8785 (ttm110) REVERT: D 96 THR cc_start: 0.9534 (m) cc_final: 0.9306 (p) REVERT: D 108 LYS cc_start: 0.9470 (mtpp) cc_final: 0.9136 (ptpp) REVERT: E 50 GLU cc_start: 0.9410 (pt0) cc_final: 0.8917 (pt0) REVERT: E 122 LYS cc_start: 0.9223 (ptmt) cc_final: 0.8893 (ptmt) REVERT: E 125 GLN cc_start: 0.9424 (mt0) cc_final: 0.8966 (mp10) REVERT: F 31 LYS cc_start: 0.9580 (tttp) cc_final: 0.9343 (tttm) REVERT: F 39 ARG cc_start: 0.9346 (mmt90) cc_final: 0.8828 (mmt90) REVERT: F 44 LYS cc_start: 0.9307 (tptm) cc_final: 0.9031 (tppp) REVERT: F 78 ARG cc_start: 0.8896 (mtm110) cc_final: 0.8462 (mtm110) REVERT: F 84 MET cc_start: 0.8753 (mmm) cc_final: 0.8384 (mmm) REVERT: F 95 ARG cc_start: 0.8845 (mtp85) cc_final: 0.8577 (mtt90) REVERT: G 32 ARG cc_start: 0.9270 (ttp80) cc_final: 0.8933 (tmm-80) REVERT: G 38 ASN cc_start: 0.9254 (m-40) cc_final: 0.8974 (m-40) REVERT: G 39 TYR cc_start: 0.9424 (m-80) cc_final: 0.9125 (m-80) REVERT: G 42 ARG cc_start: 0.8834 (ptp-110) cc_final: 0.7802 (ptm-80) REVERT: G 77 ARG cc_start: 0.8611 (mtt180) cc_final: 0.8199 (mpt-90) REVERT: G 81 ARG cc_start: 0.9168 (tpt90) cc_final: 0.8895 (tpt170) REVERT: G 90 ASP cc_start: 0.8547 (t0) cc_final: 0.8202 (t0) REVERT: H 37 TYR cc_start: 0.9477 (m-80) cc_final: 0.9109 (m-80) REVERT: H 42 TYR cc_start: 0.8726 (t80) cc_final: 0.8452 (t80) REVERT: H 59 MET cc_start: 0.8911 (tpp) cc_final: 0.8624 (tpp) REVERT: H 70 PHE cc_start: 0.9326 (t80) cc_final: 0.9120 (t80) REVERT: H 84 ASN cc_start: 0.9308 (OUTLIER) cc_final: 0.9020 (m110) REVERT: H 92 ARG cc_start: 0.8874 (mtp-110) cc_final: 0.8219 (ttp80) REVERT: K 50 LYS cc_start: 0.9201 (mptt) cc_final: 0.8991 (mmtp) REVERT: M 77 ASP cc_start: 0.8215 (m-30) cc_final: 0.7529 (p0) REVERT: M 104 MET cc_start: 0.8978 (mmm) cc_final: 0.8744 (mmm) REVERT: N 38 MET cc_start: 0.3855 (ppp) cc_final: 0.3433 (ppp) REVERT: N 79 ASN cc_start: 0.6457 (p0) cc_final: 0.6095 (p0) outliers start: 29 outliers final: 21 residues processed: 468 average time/residue: 0.1226 time to fit residues: 80.4178 Evaluate side-chains 447 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 424 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain N residue 37 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 29 optimal weight: 0.7980 chunk 110 optimal weight: 50.0000 chunk 56 optimal weight: 0.0570 chunk 129 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 99 optimal weight: 30.0000 chunk 41 optimal weight: 0.8980 chunk 126 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** K 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 ASN ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.052793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.042250 restraints weight = 92436.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.043548 restraints weight = 41961.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.044429 restraints weight = 24757.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.045017 restraints weight = 17127.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.045458 restraints weight = 13494.831| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 15436 Z= 0.159 Angle : 0.753 14.556 22114 Z= 0.406 Chirality : 0.045 0.285 2519 Planarity : 0.005 0.065 1788 Dihedral : 29.559 172.271 4403 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.39 % Favored : 96.52 % Rotamer: Outliers : 4.82 % Allowed : 25.63 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.25), residues: 1062 helix: 0.90 (0.20), residues: 660 sheet: 0.59 (1.19), residues: 24 loop : -1.04 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 112 TYR 0.037 0.002 TYR D 83 PHE 0.028 0.002 PHE F 61 TRP 0.006 0.001 TRP N 141 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 (15420) covalent geometry : angle 0.72231 / 0.40 (22096) hydrogen bonds : bond 0.04736 / 3.18 ( 872) hydrogen bonds : angle 3.75372 / 2.66 ( 2220) metal coordination : bond 0.02680 / 1.39 ( 16) metal coordination : angle 7.46640 / 4.25 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 458 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9205 (pt0) cc_final: 0.8833 (pt0) REVERT: A 105 GLU cc_start: 0.9019 (tp30) cc_final: 0.8557 (tp30) REVERT: A 109 LEU cc_start: 0.9303 (mp) cc_final: 0.8483 (mp) REVERT: A 112 ILE cc_start: 0.9312 (pt) cc_final: 0.9068 (mt) REVERT: A 120 MET cc_start: 0.8513 (mmm) cc_final: 0.8123 (mtp) REVERT: A 129 ARG cc_start: 0.8698 (tpm170) cc_final: 0.8426 (tpm170) REVERT: B 35 ARG cc_start: 0.8960 (mtm-85) cc_final: 0.8561 (ttm110) REVERT: B 39 ARG cc_start: 0.9400 (mmt180) cc_final: 0.8401 (mmt180) REVERT: B 49 LEU cc_start: 0.8989 (mm) cc_final: 0.8728 (tp) REVERT: B 67 ARG cc_start: 0.8719 (ttm110) cc_final: 0.8500 (ttm110) REVERT: B 79 LYS cc_start: 0.9066 (mtmt) cc_final: 0.8656 (ptpt) REVERT: B 88 TYR cc_start: 0.9113 (m-80) cc_final: 0.8823 (m-80) REVERT: C 15 LYS cc_start: 0.8429 (mmmt) cc_final: 0.8212 (mmmt) REVERT: C 38 ASN cc_start: 0.8856 (m-40) cc_final: 0.8635 (m-40) REVERT: C 56 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8913 (mt-10) REVERT: C 68 ASN cc_start: 0.9411 (m-40) cc_final: 0.9194 (m110) REVERT: C 101 THR cc_start: 0.9035 (m) cc_final: 0.8530 (p) REVERT: D 47 GLN cc_start: 0.9292 (tm-30) cc_final: 0.8953 (tm-30) REVERT: D 68 ASP cc_start: 0.9367 (t0) cc_final: 0.9044 (t0) REVERT: D 71 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8791 (tm-30) REVERT: D 93 GLU cc_start: 0.9001 (pm20) cc_final: 0.8555 (pm20) REVERT: D 96 THR cc_start: 0.9562 (m) cc_final: 0.9291 (p) REVERT: E 50 GLU cc_start: 0.9394 (pt0) cc_final: 0.9163 (pt0) REVERT: E 125 GLN cc_start: 0.9431 (mt0) cc_final: 0.9032 (mp10) REVERT: E 133 GLU cc_start: 0.8412 (mp0) cc_final: 0.8163 (mp0) REVERT: F 31 LYS cc_start: 0.9581 (tttp) cc_final: 0.9339 (tttp) REVERT: F 35 ARG cc_start: 0.9293 (ttm-80) cc_final: 0.8518 (ttm-80) REVERT: F 44 LYS cc_start: 0.9318 (tptm) cc_final: 0.9083 (tppp) REVERT: F 51 TYR cc_start: 0.8534 (m-80) cc_final: 0.8196 (m-80) REVERT: F 59 LYS cc_start: 0.9455 (ptmm) cc_final: 0.8995 (ptmm) REVERT: F 63 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8562 (mp0) REVERT: F 78 ARG cc_start: 0.8829 (mtm110) cc_final: 0.8407 (mtm110) REVERT: F 84 MET cc_start: 0.8581 (mmm) cc_final: 0.8120 (mmm) REVERT: F 95 ARG cc_start: 0.8810 (mtp85) cc_final: 0.8489 (mtt90) REVERT: G 25 PHE cc_start: 0.9157 (m-80) cc_final: 0.8883 (m-80) REVERT: G 32 ARG cc_start: 0.9382 (ttp80) cc_final: 0.8895 (tmm-80) REVERT: G 35 ARG cc_start: 0.8722 (mtm110) cc_final: 0.8464 (mtp-110) REVERT: G 38 ASN cc_start: 0.9183 (m-40) cc_final: 0.8895 (m-40) REVERT: G 39 TYR cc_start: 0.9443 (m-80) cc_final: 0.9028 (m-80) REVERT: G 42 ARG cc_start: 0.8864 (ptp-110) cc_final: 0.8038 (ptm160) REVERT: G 81 ARG cc_start: 0.9170 (tpt170) cc_final: 0.8916 (tpt170) REVERT: G 93 LEU cc_start: 0.9679 (mt) cc_final: 0.9364 (mp) REVERT: H 37 TYR cc_start: 0.9493 (m-80) cc_final: 0.9082 (m-80) REVERT: H 42 TYR cc_start: 0.8801 (t80) cc_final: 0.8531 (t80) REVERT: H 59 MET cc_start: 0.8901 (tpp) cc_final: 0.8579 (tpp) REVERT: H 70 PHE cc_start: 0.9359 (t80) cc_final: 0.9079 (t80) REVERT: H 92 ARG cc_start: 0.8824 (mtp-110) cc_final: 0.8048 (ttp80) REVERT: H 96 THR cc_start: 0.9614 (m) cc_final: 0.9322 (p) REVERT: K 50 LYS cc_start: 0.9245 (mptt) cc_final: 0.8991 (mmtp) REVERT: N 38 MET cc_start: 0.3883 (ppp) cc_final: 0.3444 (ppp) REVERT: N 79 ASN cc_start: 0.6432 (p0) cc_final: 0.6009 (p0) outliers start: 44 outliers final: 28 residues processed: 471 average time/residue: 0.1336 time to fit residues: 87.7386 Evaluate side-chains 457 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 428 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain M residue 55 ASN Chi-restraints excluded: chain N residue 31 PHE Chi-restraints excluded: chain N residue 37 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 38 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 chunk 108 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 GLN ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.052975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.042382 restraints weight = 93285.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.043654 restraints weight = 43108.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.044497 restraints weight = 25804.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.045110 restraints weight = 18215.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.045260 restraints weight = 14318.266| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 15436 Z= 0.160 Angle : 0.756 13.964 22114 Z= 0.405 Chirality : 0.046 0.464 2519 Planarity : 0.005 0.059 1788 Dihedral : 29.600 172.660 4403 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.14 % Rotamer: Outliers : 4.16 % Allowed : 29.13 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.25), residues: 1062 helix: 0.84 (0.20), residues: 662 sheet: 0.65 (1.19), residues: 24 loop : -1.05 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 92 TYR 0.030 0.002 TYR H 83 PHE 0.028 0.002 PHE F 61 TRP 0.005 0.001 TRP N 141 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 (15420) covalent geometry : angle 0.72687 / 0.40 (22096) hydrogen bonds : bond 0.04632 / 3.10 ( 872) hydrogen bonds : angle 3.73065 / 2.65 ( 2220) metal coordination : bond 0.02631 / 1.35 ( 16) metal coordination : angle 7.34528 / 4.12 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 446 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 THR cc_start: 0.9451 (m) cc_final: 0.9231 (p) REVERT: A 94 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8578 (mm-30) REVERT: A 105 GLU cc_start: 0.8949 (tp30) cc_final: 0.8508 (tp30) REVERT: A 109 LEU cc_start: 0.9373 (mp) cc_final: 0.8535 (mp) REVERT: A 120 MET cc_start: 0.8462 (mmm) cc_final: 0.8073 (mtp) REVERT: A 129 ARG cc_start: 0.8736 (tpm170) cc_final: 0.8425 (tpm170) REVERT: B 49 LEU cc_start: 0.8902 (mm) cc_final: 0.8665 (tp) REVERT: B 88 TYR cc_start: 0.9159 (m-80) cc_final: 0.8796 (m-80) REVERT: C 56 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8718 (mt-10) REVERT: C 68 ASN cc_start: 0.9363 (m-40) cc_final: 0.9138 (m110) REVERT: C 101 THR cc_start: 0.9037 (m) cc_final: 0.8502 (p) REVERT: D 47 GLN cc_start: 0.9297 (tm-30) cc_final: 0.8926 (tm-30) REVERT: D 59 MET cc_start: 0.9618 (tpt) cc_final: 0.9372 (tpt) REVERT: D 68 ASP cc_start: 0.9360 (t0) cc_final: 0.9043 (t0) REVERT: D 96 THR cc_start: 0.9550 (m) cc_final: 0.9315 (p) REVERT: E 50 GLU cc_start: 0.9354 (pt0) cc_final: 0.9134 (pt0) REVERT: E 125 GLN cc_start: 0.9420 (mt0) cc_final: 0.9021 (mp10) REVERT: E 133 GLU cc_start: 0.8411 (mp0) cc_final: 0.8161 (mp0) REVERT: F 31 LYS cc_start: 0.9569 (tttp) cc_final: 0.9280 (tttp) REVERT: F 35 ARG cc_start: 0.9244 (ttm-80) cc_final: 0.8587 (ttm-80) REVERT: F 44 LYS cc_start: 0.9402 (tptm) cc_final: 0.9183 (tppp) REVERT: F 78 ARG cc_start: 0.8816 (mtm110) cc_final: 0.8429 (mtm110) REVERT: F 84 MET cc_start: 0.8543 (mmm) cc_final: 0.8074 (mmm) REVERT: F 95 ARG cc_start: 0.8759 (mtp85) cc_final: 0.8456 (mtt90) REVERT: G 25 PHE cc_start: 0.9097 (m-80) cc_final: 0.8861 (m-80) REVERT: G 35 ARG cc_start: 0.8719 (mtm110) cc_final: 0.8475 (mtp-110) REVERT: G 38 ASN cc_start: 0.9155 (m-40) cc_final: 0.8876 (m-40) REVERT: G 39 TYR cc_start: 0.9424 (m-80) cc_final: 0.9022 (m-80) REVERT: G 42 ARG cc_start: 0.8813 (ptp-110) cc_final: 0.8044 (ptm160) REVERT: G 90 ASP cc_start: 0.8553 (t0) cc_final: 0.8241 (t0) REVERT: G 93 LEU cc_start: 0.9689 (mt) cc_final: 0.9482 (mp) REVERT: H 35 GLU cc_start: 0.8242 (tp30) cc_final: 0.7444 (tp30) REVERT: H 37 TYR cc_start: 0.9425 (m-80) cc_final: 0.8975 (m-80) REVERT: H 42 TYR cc_start: 0.8737 (t80) cc_final: 0.8494 (t80) REVERT: H 80 LEU cc_start: 0.9544 (mt) cc_final: 0.9235 (mt) REVERT: H 92 ARG cc_start: 0.8882 (mtp-110) cc_final: 0.8192 (ttp80) REVERT: H 96 THR cc_start: 0.9609 (m) cc_final: 0.9321 (p) REVERT: K 50 LYS cc_start: 0.9200 (mptt) cc_final: 0.8926 (mmtp) REVERT: M 104 MET cc_start: 0.8863 (mmm) cc_final: 0.8511 (mmt) REVERT: N 38 MET cc_start: 0.4100 (ppp) cc_final: 0.3658 (ppp) REVERT: N 140 GLU cc_start: 0.9215 (pt0) cc_final: 0.9008 (pt0) outliers start: 38 outliers final: 28 residues processed: 457 average time/residue: 0.1272 time to fit residues: 81.4590 Evaluate side-chains 445 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 417 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 64 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 89 optimal weight: 20.0000 chunk 73 optimal weight: 30.0000 chunk 11 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 90 optimal weight: 20.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.052494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.042124 restraints weight = 93589.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.043384 restraints weight = 43503.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.044176 restraints weight = 26022.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.044791 restraints weight = 18594.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.044931 restraints weight = 14564.164| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 15436 Z= 0.161 Angle : 0.758 14.296 22114 Z= 0.406 Chirality : 0.045 0.345 2519 Planarity : 0.005 0.044 1788 Dihedral : 29.697 172.992 4403 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.95 % Rotamer: Outliers : 4.27 % Allowed : 30.01 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.25), residues: 1062 helix: 0.88 (0.20), residues: 661 sheet: 0.66 (1.18), residues: 24 loop : -1.01 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 92 TYR 0.036 0.002 TYR H 83 PHE 0.030 0.002 PHE F 61 TRP 0.004 0.001 TRP N 141 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (15420) covalent geometry : angle 0.73020 / 0.40 (22096) hydrogen bonds : bond 0.04691 / 3.13 ( 872) hydrogen bonds : angle 3.72104 / 2.64 ( 2220) metal coordination : bond 0.02330 / 1.20 ( 16) metal coordination : angle 7.11579 / 3.93 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 435 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8668 (tp40) cc_final: 0.8349 (tp40) REVERT: A 94 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8609 (mm-30) REVERT: A 120 MET cc_start: 0.8443 (mmm) cc_final: 0.8062 (mtp) REVERT: A 129 ARG cc_start: 0.8769 (tpm170) cc_final: 0.8429 (tpm170) REVERT: B 49 LEU cc_start: 0.8900 (mm) cc_final: 0.8602 (tp) REVERT: B 88 TYR cc_start: 0.9189 (m-80) cc_final: 0.8796 (m-80) REVERT: C 38 ASN cc_start: 0.8975 (m-40) cc_final: 0.8325 (t0) REVERT: C 56 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8954 (mt-10) REVERT: C 68 ASN cc_start: 0.9312 (m-40) cc_final: 0.9091 (m110) REVERT: C 101 THR cc_start: 0.9037 (m) cc_final: 0.8525 (p) REVERT: D 47 GLN cc_start: 0.9309 (tm-30) cc_final: 0.8950 (tm-30) REVERT: D 59 MET cc_start: 0.9583 (tpt) cc_final: 0.9369 (tpt) REVERT: D 68 ASP cc_start: 0.9382 (t0) cc_final: 0.9067 (t0) REVERT: D 93 GLU cc_start: 0.8957 (pm20) cc_final: 0.8360 (pm20) REVERT: D 96 THR cc_start: 0.9555 (m) cc_final: 0.9330 (p) REVERT: D 105 GLU cc_start: 0.8468 (pm20) cc_final: 0.7781 (pm20) REVERT: D 108 LYS cc_start: 0.9459 (ptpp) cc_final: 0.9126 (pttp) REVERT: E 50 GLU cc_start: 0.9328 (pt0) cc_final: 0.9110 (pt0) REVERT: E 79 LYS cc_start: 0.9191 (tptm) cc_final: 0.8892 (tptp) REVERT: E 122 LYS cc_start: 0.9227 (ptmt) cc_final: 0.8769 (ptmt) REVERT: E 125 GLN cc_start: 0.9433 (mt0) cc_final: 0.9029 (mp10) REVERT: E 133 GLU cc_start: 0.8469 (mp0) cc_final: 0.8208 (mp0) REVERT: F 31 LYS cc_start: 0.9576 (tttp) cc_final: 0.9266 (tttm) REVERT: F 35 ARG cc_start: 0.9284 (ttm-80) cc_final: 0.8553 (ttm-80) REVERT: F 44 LYS cc_start: 0.9426 (tptm) cc_final: 0.9193 (tppp) REVERT: F 51 TYR cc_start: 0.8444 (m-80) cc_final: 0.8099 (m-80) REVERT: F 78 ARG cc_start: 0.8826 (mtm110) cc_final: 0.8245 (mtm110) REVERT: F 84 MET cc_start: 0.8599 (mmm) cc_final: 0.7226 (mmm) REVERT: F 88 TYR cc_start: 0.8841 (m-10) cc_final: 0.7471 (m-80) REVERT: F 92 ARG cc_start: 0.9335 (mtp-110) cc_final: 0.8874 (ttt-90) REVERT: F 95 ARG cc_start: 0.8776 (mtp85) cc_final: 0.8513 (mtt90) REVERT: G 25 PHE cc_start: 0.9108 (m-80) cc_final: 0.8852 (m-80) REVERT: G 32 ARG cc_start: 0.9422 (ptt180) cc_final: 0.8837 (ttp80) REVERT: G 35 ARG cc_start: 0.8711 (mtm110) cc_final: 0.8362 (mtp-110) REVERT: G 36 LYS cc_start: 0.9239 (mtmt) cc_final: 0.8988 (mmtm) REVERT: G 38 ASN cc_start: 0.9240 (m-40) cc_final: 0.8760 (m-40) REVERT: G 42 ARG cc_start: 0.8789 (ptp-110) cc_final: 0.8030 (ptm160) REVERT: G 75 LYS cc_start: 0.9245 (mmtp) cc_final: 0.8946 (mmtm) REVERT: H 35 GLU cc_start: 0.8398 (tp30) cc_final: 0.7978 (tp30) REVERT: H 37 TYR cc_start: 0.9417 (m-80) cc_final: 0.9018 (m-80) REVERT: H 42 TYR cc_start: 0.8827 (t80) cc_final: 0.8538 (t80) REVERT: H 70 PHE cc_start: 0.9359 (t80) cc_final: 0.9026 (t80) REVERT: H 92 ARG cc_start: 0.8865 (mtp-110) cc_final: 0.8149 (ttp80) REVERT: H 96 THR cc_start: 0.9611 (m) cc_final: 0.9318 (p) REVERT: M 104 MET cc_start: 0.8928 (mmm) cc_final: 0.8694 (mmm) REVERT: N 38 MET cc_start: 0.4116 (ppp) cc_final: 0.3710 (ppp) REVERT: N 140 GLU cc_start: 0.9168 (pt0) cc_final: 0.8876 (pt0) REVERT: N 143 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8552 (mm-40) outliers start: 39 outliers final: 29 residues processed: 449 average time/residue: 0.1349 time to fit residues: 84.8121 Evaluate side-chains 449 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 419 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 143 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 68 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 101 optimal weight: 30.0000 chunk 114 optimal weight: 40.0000 chunk 3 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.050749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.040346 restraints weight = 94432.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.041545 restraints weight = 44004.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.042365 restraints weight = 26603.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.042962 restraints weight = 18780.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.043352 restraints weight = 14703.098| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 15436 Z= 0.222 Angle : 0.807 16.601 22114 Z= 0.428 Chirality : 0.047 0.350 2519 Planarity : 0.005 0.052 1788 Dihedral : 29.955 172.820 4403 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.95 % Rotamer: Outliers : 5.26 % Allowed : 30.67 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.25), residues: 1062 helix: 0.95 (0.20), residues: 661 sheet: 0.74 (1.22), residues: 24 loop : -0.98 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 112 TYR 0.027 0.002 TYR H 83 PHE 0.025 0.002 PHE F 61 TRP 0.004 0.001 TRP N 141 HIS 0.005 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.22 (15420) covalent geometry : angle 0.77806 / 0.43 (22096) hydrogen bonds : bond 0.05714 / 3.80 ( 872) hydrogen bonds : angle 3.87014 / 2.74 ( 2220) metal coordination : bond 0.02343 / 1.28 ( 16) metal coordination : angle 7.55711 / 3.95 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 424 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.8332 (m-80) cc_final: 0.7877 (m-80) REVERT: A 94 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8664 (mm-30) REVERT: A 112 ILE cc_start: 0.9420 (pt) cc_final: 0.9181 (mt) REVERT: A 120 MET cc_start: 0.8607 (mmm) cc_final: 0.8305 (mtp) REVERT: A 129 ARG cc_start: 0.8826 (tpm170) cc_final: 0.8491 (tpm170) REVERT: B 49 LEU cc_start: 0.8962 (mm) cc_final: 0.8635 (tp) REVERT: B 88 TYR cc_start: 0.9201 (m-80) cc_final: 0.8869 (m-80) REVERT: C 38 ASN cc_start: 0.8995 (m-40) cc_final: 0.8438 (t0) REVERT: C 39 TYR cc_start: 0.9252 (m-80) cc_final: 0.9011 (m-80) REVERT: C 56 GLU cc_start: 0.9261 (mt-10) cc_final: 0.8873 (mt-10) REVERT: C 68 ASN cc_start: 0.9375 (m-40) cc_final: 0.8457 (m110) REVERT: C 75 LYS cc_start: 0.8682 (mmmm) cc_final: 0.8460 (mmmm) REVERT: C 101 THR cc_start: 0.9023 (m) cc_final: 0.8564 (p) REVERT: C 104 GLN cc_start: 0.8185 (mp10) cc_final: 0.7742 (mp10) REVERT: D 46 LYS cc_start: 0.9703 (mmmt) cc_final: 0.9488 (mmmt) REVERT: D 47 GLN cc_start: 0.9332 (tm-30) cc_final: 0.8941 (tm-30) REVERT: D 68 ASP cc_start: 0.9412 (t0) cc_final: 0.9090 (t0) REVERT: D 83 TYR cc_start: 0.7495 (m-80) cc_final: 0.6837 (m-80) REVERT: D 96 THR cc_start: 0.9577 (m) cc_final: 0.9309 (p) REVERT: D 105 GLU cc_start: 0.8409 (pm20) cc_final: 0.7901 (pm20) REVERT: D 108 LYS cc_start: 0.9467 (ptpp) cc_final: 0.9123 (pttp) REVERT: E 50 GLU cc_start: 0.9307 (pt0) cc_final: 0.9036 (pt0) REVERT: E 79 LYS cc_start: 0.9294 (tptm) cc_final: 0.8964 (tptt) REVERT: E 122 LYS cc_start: 0.9256 (ptmt) cc_final: 0.8822 (ptmt) REVERT: E 125 GLN cc_start: 0.9475 (mt0) cc_final: 0.9098 (mp10) REVERT: E 133 GLU cc_start: 0.8535 (mp0) cc_final: 0.8233 (mp0) REVERT: F 44 LYS cc_start: 0.9437 (tptm) cc_final: 0.8717 (tppp) REVERT: F 78 ARG cc_start: 0.8943 (mtm110) cc_final: 0.8217 (mtm110) REVERT: F 82 THR cc_start: 0.9410 (m) cc_final: 0.8904 (m) REVERT: F 84 MET cc_start: 0.8725 (mmm) cc_final: 0.8323 (tpp) REVERT: F 95 ARG cc_start: 0.8849 (mtp85) cc_final: 0.8513 (mtt90) REVERT: G 25 PHE cc_start: 0.9209 (m-80) cc_final: 0.8889 (m-80) REVERT: G 32 ARG cc_start: 0.9409 (ptt180) cc_final: 0.9135 (ptt180) REVERT: G 38 ASN cc_start: 0.9154 (m-40) cc_final: 0.8779 (m110) REVERT: G 42 ARG cc_start: 0.8805 (ptp-110) cc_final: 0.8051 (ptm160) REVERT: G 75 LYS cc_start: 0.9251 (mmtp) cc_final: 0.9008 (mmtm) REVERT: H 33 ARG cc_start: 0.8040 (ttm170) cc_final: 0.7608 (mtt180) REVERT: H 35 GLU cc_start: 0.8345 (tp30) cc_final: 0.8077 (tp30) REVERT: H 37 TYR cc_start: 0.9433 (m-80) cc_final: 0.9098 (m-80) REVERT: H 42 TYR cc_start: 0.8855 (t80) cc_final: 0.8583 (t80) REVERT: H 70 PHE cc_start: 0.9409 (t80) cc_final: 0.9135 (t80) REVERT: H 83 TYR cc_start: 0.8957 (m-80) cc_final: 0.8753 (m-80) REVERT: M 104 MET cc_start: 0.9013 (mmm) cc_final: 0.8765 (mmm) REVERT: N 29 ASP cc_start: 0.6637 (t70) cc_final: 0.6176 (p0) REVERT: N 38 MET cc_start: 0.3719 (ppp) cc_final: 0.3364 (ppp) REVERT: N 143 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8536 (mm-40) outliers start: 48 outliers final: 37 residues processed: 438 average time/residue: 0.1361 time to fit residues: 82.9921 Evaluate side-chains 437 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 399 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 143 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 111 optimal weight: 0.0270 chunk 74 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 118 optimal weight: 0.0370 chunk 31 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 101 optimal weight: 30.0000 chunk 56 optimal weight: 5.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN E 93 GLN E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 ASN ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.052239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.041785 restraints weight = 92076.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.043016 restraints weight = 42558.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.043819 restraints weight = 25610.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.044432 restraints weight = 18308.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.044842 restraints weight = 14327.167| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 15436 Z= 0.159 Angle : 0.794 14.449 22114 Z= 0.420 Chirality : 0.046 0.365 2519 Planarity : 0.005 0.055 1788 Dihedral : 29.909 173.296 4403 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 3.83 % Allowed : 32.53 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.25), residues: 1062 helix: 0.94 (0.20), residues: 663 sheet: 0.59 (1.20), residues: 24 loop : -0.93 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 71 TYR 0.023 0.002 TYR H 83 PHE 0.036 0.003 PHE A 67 TRP 0.006 0.001 TRP N 141 HIS 0.008 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (15420) covalent geometry : angle 0.76835 / 0.42 (22096) hydrogen bonds : bond 0.04594 / 3.10 ( 872) hydrogen bonds : angle 3.74166 / 2.64 ( 2220) metal coordination : bond 0.02542 / 1.27 ( 16) metal coordination : angle 7.02786 / 4.04 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 430 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.8325 (m-80) cc_final: 0.7876 (m-80) REVERT: A 94 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8688 (mm-30) REVERT: A 120 MET cc_start: 0.8445 (mmm) cc_final: 0.8100 (mtp) REVERT: A 129 ARG cc_start: 0.8808 (tpm170) cc_final: 0.8440 (tpm170) REVERT: B 49 LEU cc_start: 0.8878 (mm) cc_final: 0.8539 (tp) REVERT: B 88 TYR cc_start: 0.9137 (m-80) cc_final: 0.8769 (m-80) REVERT: C 38 ASN cc_start: 0.8977 (m-40) cc_final: 0.8436 (t0) REVERT: C 39 TYR cc_start: 0.9239 (m-80) cc_final: 0.8935 (m-80) REVERT: C 56 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8935 (mt-10) REVERT: C 68 ASN cc_start: 0.9102 (m-40) cc_final: 0.8870 (m110) REVERT: C 101 THR cc_start: 0.8937 (m) cc_final: 0.8460 (p) REVERT: C 112 GLN cc_start: 0.8629 (tp40) cc_final: 0.8425 (tp40) REVERT: D 47 GLN cc_start: 0.9336 (tm-30) cc_final: 0.8948 (tm-30) REVERT: D 68 ASP cc_start: 0.9429 (t0) cc_final: 0.9114 (t0) REVERT: D 80 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9391 (tp) REVERT: D 93 GLU cc_start: 0.8901 (pm20) cc_final: 0.8198 (pm20) REVERT: D 96 THR cc_start: 0.9535 (m) cc_final: 0.9243 (p) REVERT: D 105 GLU cc_start: 0.8455 (pm20) cc_final: 0.7861 (pm20) REVERT: D 108 LYS cc_start: 0.9483 (ptpp) cc_final: 0.9117 (pttp) REVERT: D 120 LYS cc_start: 0.9350 (tttp) cc_final: 0.9107 (ttpp) REVERT: E 122 LYS cc_start: 0.9201 (ptmt) cc_final: 0.8793 (ptmt) REVERT: E 125 GLN cc_start: 0.9483 (mt0) cc_final: 0.9123 (mp10) REVERT: E 133 GLU cc_start: 0.8601 (mp0) cc_final: 0.8326 (mp0) REVERT: F 44 LYS cc_start: 0.9405 (tptm) cc_final: 0.9076 (tppp) REVERT: F 78 ARG cc_start: 0.8881 (mtm110) cc_final: 0.8149 (mtm110) REVERT: F 82 THR cc_start: 0.9390 (m) cc_final: 0.8992 (m) REVERT: F 84 MET cc_start: 0.8718 (mmm) cc_final: 0.8137 (mmm) REVERT: F 92 ARG cc_start: 0.9175 (mmm-85) cc_final: 0.8882 (ttt-90) REVERT: F 95 ARG cc_start: 0.8773 (mtp85) cc_final: 0.8527 (mtt90) REVERT: G 25 PHE cc_start: 0.9155 (m-80) cc_final: 0.8850 (m-80) REVERT: G 36 LYS cc_start: 0.9227 (mtmt) cc_final: 0.8958 (mtmt) REVERT: G 38 ASN cc_start: 0.9108 (m-40) cc_final: 0.8710 (m-40) REVERT: H 37 TYR cc_start: 0.9431 (m-80) cc_final: 0.9024 (m-80) REVERT: H 42 TYR cc_start: 0.8801 (t80) cc_final: 0.8516 (t80) REVERT: H 70 PHE cc_start: 0.9424 (t80) cc_final: 0.9146 (t80) REVERT: H 92 ARG cc_start: 0.8912 (mtp-110) cc_final: 0.8130 (ttp80) REVERT: M 104 MET cc_start: 0.9026 (mmm) cc_final: 0.8811 (mmm) REVERT: N 38 MET cc_start: 0.4105 (ppp) cc_final: 0.3753 (ppp) REVERT: N 140 GLU cc_start: 0.9195 (pt0) cc_final: 0.8927 (pt0) REVERT: N 143 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8525 (mm-40) outliers start: 35 outliers final: 24 residues processed: 442 average time/residue: 0.1386 time to fit residues: 86.5410 Evaluate side-chains 426 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 400 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 143 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 17 optimal weight: 0.0770 chunk 18 optimal weight: 0.0370 chunk 118 optimal weight: 0.0670 chunk 89 optimal weight: 20.0000 chunk 46 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 93 GLN E 108 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.053125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.042647 restraints weight = 92650.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.043900 restraints weight = 43211.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.044751 restraints weight = 25905.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.045349 restraints weight = 18289.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.045767 restraints weight = 14383.481| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 15436 Z= 0.162 Angle : 0.846 18.967 22114 Z= 0.439 Chirality : 0.047 0.435 2519 Planarity : 0.005 0.055 1788 Dihedral : 29.838 174.116 4403 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.58 % Favored : 96.33 % Rotamer: Outliers : 3.29 % Allowed : 35.05 % Favored : 61.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.25), residues: 1062 helix: 0.79 (0.20), residues: 664 sheet: 0.57 (1.18), residues: 24 loop : -0.99 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 112 TYR 0.044 0.002 TYR H 83 PHE 0.030 0.002 PHE E 67 TRP 0.004 0.001 TRP N 141 HIS 0.007 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (15420) covalent geometry : angle 0.82283 / 0.44 (22096) hydrogen bonds : bond 0.04559 / 3.09 ( 872) hydrogen bonds : angle 3.76310 / 2.66 ( 2220) metal coordination : bond 0.02479 / 1.24 ( 16) metal coordination : angle 6.89718 / 3.69 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 432 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.8259 (m-80) cc_final: 0.7816 (m-80) REVERT: A 94 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8360 (mt-10) REVERT: A 120 MET cc_start: 0.8382 (mmm) cc_final: 0.7999 (mtp) REVERT: A 129 ARG cc_start: 0.8833 (tpm170) cc_final: 0.8462 (tpm170) REVERT: B 49 LEU cc_start: 0.8858 (mm) cc_final: 0.8539 (tp) REVERT: B 52 GLU cc_start: 0.8309 (pm20) cc_final: 0.8039 (pm20) REVERT: B 53 GLU cc_start: 0.7828 (pm20) cc_final: 0.7597 (pm20) REVERT: B 88 TYR cc_start: 0.9156 (m-80) cc_final: 0.8782 (m-80) REVERT: C 38 ASN cc_start: 0.8939 (m-40) cc_final: 0.8433 (t0) REVERT: C 39 TYR cc_start: 0.9210 (m-80) cc_final: 0.8901 (m-80) REVERT: C 56 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8909 (mt-10) REVERT: C 101 THR cc_start: 0.8869 (m) cc_final: 0.8369 (p) REVERT: C 104 GLN cc_start: 0.8296 (mp10) cc_final: 0.7995 (mp10) REVERT: C 112 GLN cc_start: 0.8539 (tp40) cc_final: 0.8333 (tp40) REVERT: D 47 GLN cc_start: 0.9308 (tm-30) cc_final: 0.8907 (tm-30) REVERT: D 59 MET cc_start: 0.9605 (tpt) cc_final: 0.9379 (tpt) REVERT: D 68 ASP cc_start: 0.9419 (t0) cc_final: 0.9179 (t0) REVERT: D 80 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9375 (tp) REVERT: D 93 GLU cc_start: 0.8914 (pm20) cc_final: 0.8207 (pm20) REVERT: D 96 THR cc_start: 0.9557 (m) cc_final: 0.9300 (p) REVERT: D 105 GLU cc_start: 0.8228 (pm20) cc_final: 0.7621 (pm20) REVERT: D 108 LYS cc_start: 0.9471 (ptpp) cc_final: 0.9075 (pttp) REVERT: D 120 LYS cc_start: 0.9344 (tttp) cc_final: 0.9086 (ttpp) REVERT: E 79 LYS cc_start: 0.9248 (tptm) cc_final: 0.8985 (tptt) REVERT: E 120 MET cc_start: 0.8652 (mmm) cc_final: 0.8376 (mmm) REVERT: E 122 LYS cc_start: 0.9248 (ptmt) cc_final: 0.8600 (ptmm) REVERT: E 125 GLN cc_start: 0.9496 (mt0) cc_final: 0.9102 (mp10) REVERT: E 133 GLU cc_start: 0.8601 (mp0) cc_final: 0.8344 (mp0) REVERT: F 44 LYS cc_start: 0.9301 (tptm) cc_final: 0.8915 (tppp) REVERT: F 78 ARG cc_start: 0.8809 (mtm110) cc_final: 0.8308 (mtm110) REVERT: F 79 LYS cc_start: 0.9093 (mtpp) cc_final: 0.8728 (mtmm) REVERT: F 82 THR cc_start: 0.9389 (m) cc_final: 0.9065 (m) REVERT: F 84 MET cc_start: 0.8768 (mmm) cc_final: 0.8068 (mmm) REVERT: F 92 ARG cc_start: 0.9203 (mmm-85) cc_final: 0.8803 (ttt-90) REVERT: F 95 ARG cc_start: 0.8766 (mtp85) cc_final: 0.8427 (mtt90) REVERT: G 25 PHE cc_start: 0.9108 (m-80) cc_final: 0.8826 (m-80) REVERT: G 36 LYS cc_start: 0.9240 (mtmt) cc_final: 0.8926 (mtmt) REVERT: G 38 ASN cc_start: 0.9131 (m-40) cc_final: 0.8726 (m-40) REVERT: G 57 TYR cc_start: 0.9306 (t80) cc_final: 0.8553 (t80) REVERT: G 61 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8358 (mp0) REVERT: G 90 ASP cc_start: 0.8634 (t0) cc_final: 0.8203 (t0) REVERT: H 37 TYR cc_start: 0.9371 (m-80) cc_final: 0.9100 (m-80) REVERT: H 42 TYR cc_start: 0.8810 (t80) cc_final: 0.8533 (t80) REVERT: H 70 PHE cc_start: 0.9420 (t80) cc_final: 0.9125 (t80) REVERT: H 83 TYR cc_start: 0.8577 (m-10) cc_final: 0.8214 (m-80) REVERT: H 92 ARG cc_start: 0.8957 (mtp-110) cc_final: 0.8180 (ttp80) REVERT: H 95 GLN cc_start: 0.9436 (pt0) cc_final: 0.9234 (tt0) REVERT: K 43 PHE cc_start: 0.7850 (m-10) cc_final: 0.7363 (m-80) REVERT: N 29 ASP cc_start: 0.6536 (t70) cc_final: 0.6098 (p0) REVERT: N 38 MET cc_start: 0.4140 (ppp) cc_final: 0.3865 (ppp) REVERT: N 140 GLU cc_start: 0.9190 (pt0) cc_final: 0.8909 (pt0) REVERT: N 143 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8549 (mm-40) outliers start: 30 outliers final: 20 residues processed: 439 average time/residue: 0.1315 time to fit residues: 81.8787 Evaluate side-chains 438 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 416 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 143 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 94 optimal weight: 20.0000 chunk 26 optimal weight: 0.8980 chunk 7 optimal weight: 0.0050 chunk 93 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 6 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 79 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN C 94 ASN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 75 HIS G 68 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.052771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.042377 restraints weight = 93021.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.043603 restraints weight = 43720.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.044453 restraints weight = 26606.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.045048 restraints weight = 18614.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.045472 restraints weight = 14679.932| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 15436 Z= 0.166 Angle : 0.846 15.611 22114 Z= 0.443 Chirality : 0.047 0.410 2519 Planarity : 0.005 0.059 1788 Dihedral : 29.895 174.301 4403 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 3.61 % Allowed : 35.27 % Favored : 61.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.25), residues: 1062 helix: 0.65 (0.19), residues: 663 sheet: 0.73 (1.19), residues: 24 loop : -0.98 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 112 TYR 0.041 0.002 TYR H 83 PHE 0.073 0.002 PHE A 67 TRP 0.004 0.001 TRP N 141 HIS 0.007 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 (15420) covalent geometry : angle 0.82378 / 0.44 (22096) hydrogen bonds : bond 0.04714 / 3.22 ( 872) hydrogen bonds : angle 3.80847 / 2.69 ( 2220) metal coordination : bond 0.02324 / 1.18 ( 16) metal coordination : angle 6.79480 / 3.49 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 427 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.8235 (m-80) cc_final: 0.7806 (m-80) REVERT: A 94 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8643 (mm-30) REVERT: A 120 MET cc_start: 0.8430 (mmm) cc_final: 0.8053 (mtp) REVERT: A 129 ARG cc_start: 0.8827 (tpm170) cc_final: 0.8443 (tpm170) REVERT: B 49 LEU cc_start: 0.8827 (mm) cc_final: 0.8530 (tp) REVERT: B 52 GLU cc_start: 0.8272 (pm20) cc_final: 0.8002 (pm20) REVERT: B 53 GLU cc_start: 0.7801 (pm20) cc_final: 0.7600 (pm20) REVERT: B 88 TYR cc_start: 0.9185 (m-80) cc_final: 0.8753 (m-80) REVERT: C 38 ASN cc_start: 0.8927 (m-40) cc_final: 0.8596 (t0) REVERT: C 39 TYR cc_start: 0.9226 (m-80) cc_final: 0.8940 (m-80) REVERT: C 56 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8890 (mt-10) REVERT: C 101 THR cc_start: 0.8877 (m) cc_final: 0.8437 (p) REVERT: C 104 GLN cc_start: 0.8241 (mp10) cc_final: 0.7953 (mp10) REVERT: D 40 TYR cc_start: 0.8607 (m-80) cc_final: 0.8015 (m-80) REVERT: D 47 GLN cc_start: 0.9344 (tm-30) cc_final: 0.8993 (tm-30) REVERT: D 59 MET cc_start: 0.9537 (tpt) cc_final: 0.9307 (tpt) REVERT: D 68 ASP cc_start: 0.9423 (t0) cc_final: 0.9177 (t0) REVERT: D 93 GLU cc_start: 0.8871 (pm20) cc_final: 0.8208 (pm20) REVERT: D 96 THR cc_start: 0.9569 (m) cc_final: 0.9349 (p) REVERT: D 105 GLU cc_start: 0.8381 (pm20) cc_final: 0.7753 (pm20) REVERT: D 108 LYS cc_start: 0.9459 (ptpp) cc_final: 0.9085 (pttp) REVERT: D 120 LYS cc_start: 0.9354 (tttp) cc_final: 0.9096 (ttpp) REVERT: E 79 LYS cc_start: 0.9248 (tptm) cc_final: 0.8993 (tptt) REVERT: E 120 MET cc_start: 0.8629 (mmm) cc_final: 0.8384 (mmm) REVERT: E 122 LYS cc_start: 0.9237 (ptmt) cc_final: 0.8745 (ptmt) REVERT: E 125 GLN cc_start: 0.9504 (mt0) cc_final: 0.9129 (mp10) REVERT: E 133 GLU cc_start: 0.8581 (mp0) cc_final: 0.8271 (mp0) REVERT: F 44 LYS cc_start: 0.9242 (tptm) cc_final: 0.8930 (tppp) REVERT: F 78 ARG cc_start: 0.8800 (mtm110) cc_final: 0.8102 (mtm110) REVERT: F 82 THR cc_start: 0.9412 (m) cc_final: 0.9058 (m) REVERT: F 84 MET cc_start: 0.8773 (mmm) cc_final: 0.7141 (mmm) REVERT: F 88 TYR cc_start: 0.8978 (m-80) cc_final: 0.8173 (m-80) REVERT: F 95 ARG cc_start: 0.8700 (mtp85) cc_final: 0.8427 (mtt90) REVERT: G 25 PHE cc_start: 0.9096 (m-80) cc_final: 0.8836 (m-80) REVERT: G 36 LYS cc_start: 0.9246 (mtmt) cc_final: 0.8932 (mtmt) REVERT: G 38 ASN cc_start: 0.9063 (m-40) cc_final: 0.8811 (m-40) REVERT: G 57 TYR cc_start: 0.9279 (t80) cc_final: 0.8545 (t80) REVERT: G 61 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8357 (mp0) REVERT: H 37 TYR cc_start: 0.9359 (m-80) cc_final: 0.9088 (m-80) REVERT: H 42 TYR cc_start: 0.8801 (t80) cc_final: 0.8502 (t80) REVERT: H 70 PHE cc_start: 0.9440 (t80) cc_final: 0.9130 (t80) REVERT: H 92 ARG cc_start: 0.8951 (mtp-110) cc_final: 0.8253 (ttp80) REVERT: H 96 THR cc_start: 0.9598 (m) cc_final: 0.9265 (p) REVERT: N 38 MET cc_start: 0.4150 (ppp) cc_final: 0.3876 (ppp) REVERT: N 140 GLU cc_start: 0.9179 (pt0) cc_final: 0.8886 (pt0) REVERT: N 143 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8540 (mm-40) outliers start: 33 outliers final: 22 residues processed: 436 average time/residue: 0.1217 time to fit residues: 75.2655 Evaluate side-chains 431 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 408 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 143 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 113 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 108 ASN ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 ASN ** 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 = 0.3222 r_free = 0.3222 target = 0.052465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.042101 restraints weight = 94485.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.043335 restraints weight = 44607.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.044161 restraints weight = 26899.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.044780 restraints weight = 19022.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.045208 restraints weight = 14939.952| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 15436 Z= 0.175 Angle : 0.873 14.973 22114 Z= 0.450 Chirality : 0.049 0.372 2519 Planarity : 0.005 0.054 1788 Dihedral : 29.962 174.447 4403 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.95 % Rotamer: Outliers : 3.07 % Allowed : 36.14 % Favored : 60.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.25), residues: 1062 helix: 0.58 (0.20), residues: 666 sheet: 0.72 (1.18), residues: 24 loop : -0.92 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 136 TYR 0.031 0.002 TYR B 98 PHE 0.037 0.002 PHE F 61 TRP 0.008 0.001 TRP N 33 HIS 0.006 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (15420) covalent geometry : angle 0.85278 / 0.45 (22096) hydrogen bonds : bond 0.04716 / 3.20 ( 872) hydrogen bonds : angle 3.88397 / 2.73 ( 2220) metal coordination : bond 0.02302 / 1.17 ( 16) metal coordination : angle 6.66825 / 3.39 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2493.80 seconds wall clock time: 43 minutes 36.23 seconds (2616.23 seconds total)