Starting phenix.real_space_refine on Fri Jul 3 17:28:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8grq_34212/07_2026/8grq_34212.cif Found real_map, /net/cci-nas-00/data/ceres_data/8grq_34212/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8grq_34212/07_2026/8grq_34212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8grq_34212/07_2026/8grq_34212.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8grq_34212/07_2026/8grq_34212.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8grq_34212/07_2026/8grq_34212.cif" model { file = "/net/cci-nas-00/data/ceres_data/8grq_34212/07_2026/8grq_34212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8grq_34212/07_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-dev-6108/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: 3.18, per 1000 atoms: 0.22 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: 1.13 Conformation dependent library (CDL) restraints added in 485.4 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: 1.99 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: 2.58 Time building geometry restraints manager: 1.58 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: 21118 1.86 - 3.72: 914 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: 0.010 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.690 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.000 ------------------------------------------------------------------------------- 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 : 0.810 14.367 22114 Z= 0.643 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 0.79004 / 0.64 (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 : 0.428 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: 0.9174 (mp) REVERT: A 70 LEU cc_start: 0.9664 (tp) cc_final: 0.9310 (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: 0.8983 (t0) REVERT: A 112 ILE cc_start: 0.9420 (pt) cc_final: 0.9080 (mt) REVERT: A 120 MET cc_start: 0.8940 (mmm) cc_final: 0.8626 (mmm) REVERT: B 24 ASP cc_start: 0.7033 (t0) cc_final: 0.6808 (t0) REVERT: B 29 ILE cc_start: 0.9564 (mm) cc_final: 0.9317 (mp) REVERT: B 34 ILE cc_start: 0.9766 (mt) cc_final: 0.9554 (mm) REVERT: B 49 LEU cc_start: 0.9020 (mm) cc_final: 0.8592 (mt) REVERT: B 53 GLU cc_start: 0.8288 (pm20) cc_final: 0.7659 (pm20) REVERT: B 79 LYS cc_start: 0.9163 (mtmt) cc_final: 0.8750 (ptpp) REVERT: C 38 ASN cc_start: 0.8806 (m-40) cc_final: 0.8501 (p0) REVERT: C 68 ASN cc_start: 0.9307 (m-40) cc_final: 0.8786 (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: 0.8758 (p) REVERT: D 59 MET cc_start: 0.9381 (tpp) cc_final: 0.9066 (tpt) REVERT: D 68 ASP cc_start: 0.9103 (t0) cc_final: 0.8705 (t0) REVERT: D 88 THR cc_start: 0.9310 (m) cc_final: 0.9092 (p) REVERT: D 101 LEU cc_start: 0.9583 (mt) cc_final: 0.9304 (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: 0.8153 (mt) REVERT: E 97 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8288 (mt-10) REVERT: E 108 ASN cc_start: 0.9331 (t0) cc_final: 0.9103 (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: 0.9049 (mm) REVERT: F 35 ARG cc_start: 0.9221 (mtp-110) cc_final: 0.8978 (ttm-80) REVERT: F 39 ARG cc_start: 0.9116 (mmt90) cc_final: 0.8385 (mmt90) REVERT: F 44 LYS cc_start: 0.9291 (tptm) cc_final: 0.8915 (tttm) REVERT: F 49 LEU cc_start: 0.9349 (mt) cc_final: 0.8977 (mt) REVERT: F 88 TYR cc_start: 0.8981 (m-10) cc_final: 0.8417 (m-10) REVERT: G 32 ARG cc_start: 0.9137 (ttp80) cc_final: 0.8608 (tmm-80) REVERT: G 35 ARG cc_start: 0.8344 (mtm110) cc_final: 0.7473 (ptm-80) REVERT: G 36 LYS cc_start: 0.8588 (mmtm) cc_final: 0.7762 (mmtm) REVERT: G 38 ASN cc_start: 0.9048 (m-40) cc_final: 0.8826 (m-40) REVERT: G 39 TYR cc_start: 0.9372 (m-80) cc_final: 0.9029 (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: 0.8950 (t0) REVERT: H 70 PHE cc_start: 0.9371 (t80) cc_final: 0.8942 (t80) REVERT: H 83 TYR cc_start: 0.8666 (m-10) cc_final: 0.8348 (m-10) REVERT: H 86 ARG cc_start: 0.9190 (tpp80) cc_final: 0.8792 (tpp80) REVERT: H 101 LEU cc_start: 0.9258 (mp) cc_final: 0.8841 (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: 0.1503 time to fit residues: 107.7202 Evaluate side-chains 413 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 412 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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: 20.0000 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: 8.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.3162 r_free = 0.3162 target = 0.049920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.039646 restraints weight = 95429.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.040886 restraints weight = 44057.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.041567 restraints weight = 26330.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.042219 restraints weight = 19370.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.042613 restraints weight = 14717.534| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 15436 Z= 0.338 Angle : 0.881 17.920 22114 Z= 0.480 Chirality : 0.050 0.283 2519 Planarity : 0.006 0.047 1788 Dihedral : 29.495 171.408 4404 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.30 % Favored : 96.61 % Rotamer: Outliers : 5.91 % Allowed : 19.82 % Favored : 74.26 % 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: 0.16 (0.25), residues: 1062 helix: 0.73 (0.19), residues: 669 sheet: 0.57 (1.21), residues: 24 loop : -0.98 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 79 TYR 0.059 0.003 TYR D 83 PHE 0.030 0.003 PHE F 61 TRP 0.011 0.002 TRP N 141 HIS 0.012 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.34 (15420) covalent geometry : angle 0.84615 / 0.48 (22096) hydrogen bonds : bond 0.07466 / 4.98 ( 872) hydrogen bonds : angle 4.38235 / 3.12 ( 2220) metal coordination : bond 0.02325 / 1.33 ( 16) metal coordination : angle 8.58285 / 4.61 ( 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 493 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 439 time to evaluate : 0.263 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 80 THR cc_start: 0.9416 (OUTLIER) cc_final: 0.9188 (p) REVERT: A 85 GLN cc_start: 0.8960 (mt0) cc_final: 0.8534 (mt0) REVERT: A 93 GLN cc_start: 0.8897 (tp40) cc_final: 0.8644 (tp40) REVERT: A 94 GLU cc_start: 0.9281 (mm-30) cc_final: 0.8947 (mm-30) REVERT: A 105 GLU cc_start: 0.9089 (tp30) cc_final: 0.8685 (tp30) REVERT: A 112 ILE cc_start: 0.9458 (pt) cc_final: 0.9170 (mt) REVERT: A 120 MET cc_start: 0.8787 (mmm) cc_final: 0.8495 (mtp) REVERT: B 49 LEU cc_start: 0.8974 (mm) cc_final: 0.8664 (mt) REVERT: B 52 GLU cc_start: 0.8239 (pm20) cc_final: 0.7693 (pm20) REVERT: B 53 GLU cc_start: 0.7997 (pm20) cc_final: 0.7771 (pm20) REVERT: C 23 LEU cc_start: 0.9203 (mt) cc_final: 0.8996 (mt) REVERT: C 38 ASN cc_start: 0.9123 (m-40) cc_final: 0.8658 (p0) REVERT: C 68 ASN cc_start: 0.9346 (m-40) cc_final: 0.9112 (m110) REVERT: C 101 THR cc_start: 0.9146 (m) cc_final: 0.8616 (p) REVERT: C 104 GLN cc_start: 0.8352 (mp-120) cc_final: 0.8103 (mp10) REVERT: D 68 ASP cc_start: 0.9335 (t0) cc_final: 0.9045 (t0) REVERT: D 88 THR cc_start: 0.9552 (m) cc_final: 0.9330 (p) REVERT: D 89 ILE cc_start: 0.9047 (mm) cc_final: 0.8738 (mm) REVERT: D 93 GLU cc_start: 0.9179 (pm20) cc_final: 0.8815 (pm20) REVERT: D 96 THR cc_start: 0.9576 (m) cc_final: 0.9303 (p) REVERT: E 50 GLU cc_start: 0.9412 (pt0) cc_final: 0.8627 (pt0) REVERT: E 122 LYS cc_start: 0.9204 (ptmt) cc_final: 0.8964 (ptmt) REVERT: E 125 GLN cc_start: 0.9469 (mt0) cc_final: 0.9033 (mp10) REVERT: F 39 ARG cc_start: 0.9303 (mmt90) cc_final: 0.8536 (mmt90) REVERT: F 49 LEU cc_start: 0.9294 (mt) cc_final: 0.8992 (mm) REVERT: F 79 LYS cc_start: 0.9151 (mtpp) cc_final: 0.8800 (mtmm) REVERT: F 84 MET cc_start: 0.8889 (mmm) cc_final: 0.8569 (mmm) REVERT: F 88 TYR cc_start: 0.9313 (m-10) cc_final: 0.8958 (m-80) REVERT: F 95 ARG cc_start: 0.8946 (mtp85) cc_final: 0.8708 (mtt90) REVERT: G 32 ARG cc_start: 0.9293 (ttp80) cc_final: 0.8833 (ttp80) REVERT: G 36 LYS cc_start: 0.8586 (mmtm) cc_final: 0.8311 (mmtm) REVERT: G 38 ASN cc_start: 0.9380 (m-40) cc_final: 0.9143 (m-40) REVERT: G 39 TYR cc_start: 0.9497 (m-80) cc_final: 0.9266 (m-80) REVERT: G 75 LYS cc_start: 0.9358 (mttm) cc_final: 0.8889 (mmmm) REVERT: H 42 TYR cc_start: 0.8867 (t80) cc_final: 0.8652 (t80) REVERT: H 84 ASN cc_start: 0.9253 (m110) cc_final: 0.8876 (m110) REVERT: H 86 ARG cc_start: 0.9365 (tpp80) cc_final: 0.8967 (tpp80) REVERT: H 106 LEU cc_start: 0.9329 (mt) cc_final: 0.9092 (mt) REVERT: M 77 ASP cc_start: 0.8272 (m-30) cc_final: 0.7564 (p0) REVERT: M 104 MET cc_start: 0.8994 (mmm) cc_final: 0.8615 (mmt) REVERT: N 38 MET cc_start: 0.3164 (ppp) cc_final: 0.2872 (ppp) REVERT: N 79 ASN cc_start: 0.6411 (p0) cc_final: 0.6137 (p0) outliers start: 54 outliers final: 37 residues processed: 458 average time/residue: 0.1341 time to fit residues: 84.7454 Evaluate side-chains 430 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 392 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 43 VAL 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 27 VAL 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 107 VAL 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 94 ILE 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 E residue 118 THR 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 80 THR Chi-restraints excluded: chain F residue 82 THR 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: 4.9990 chunk 27 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 124 optimal weight: 30.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** 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 109 HIS ** K 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** 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 = 0.3184 r_free = 0.3184 target = 0.051033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.040352 restraints weight = 93552.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.041644 restraints weight = 42586.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.042482 restraints weight = 25314.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.043078 restraints weight = 17775.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.043493 restraints weight = 13920.507| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 15436 Z= 0.202 Angle : 0.774 15.929 22114 Z= 0.422 Chirality : 0.046 0.336 2519 Planarity : 0.005 0.044 1788 Dihedral : 29.716 172.156 4404 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.67 % Favored : 96.23 % Rotamer: Outliers : 4.05 % Allowed : 24.21 % Favored : 71.74 % 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: 0.33 (0.25), residues: 1062 helix: 0.93 (0.20), residues: 662 sheet: 0.56 (1.21), residues: 24 loop : -1.01 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 79 TYR 0.037 0.002 TYR D 83 PHE 0.026 0.002 PHE F 61 TRP 0.008 0.001 TRP N 141 HIS 0.010 0.002 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.20 (15420) covalent geometry : angle 0.73889 / 0.42 (22096) hydrogen bonds : bond 0.05410 / 3.63 ( 872) hydrogen bonds : angle 3.96649 / 2.82 ( 2220) metal coordination : bond 0.02684 / 1.40 ( 16) metal coordination : angle 8.11355 / 4.34 ( 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 475 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 438 time to evaluate : 0.329 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: symmetry clash REVERT: A 85 GLN cc_start: 0.8878 (mt0) cc_final: 0.8500 (mt0) REVERT: A 105 GLU cc_start: 0.9019 (tp30) cc_final: 0.8580 (tp30) REVERT: A 112 ILE cc_start: 0.9417 (pt) cc_final: 0.9150 (mt) REVERT: A 129 ARG cc_start: 0.8800 (tpm170) cc_final: 0.8583 (tpm170) REVERT: B 49 LEU cc_start: 0.8972 (mm) cc_final: 0.8408 (tp) REVERT: B 52 GLU cc_start: 0.8262 (pm20) cc_final: 0.7682 (pm20) REVERT: B 53 GLU cc_start: 0.7885 (pm20) cc_final: 0.7674 (pm20) REVERT: C 38 ASN cc_start: 0.9012 (m-40) cc_final: 0.8525 (p0) REVERT: C 68 ASN cc_start: 0.9386 (m-40) cc_final: 0.9139 (m110) REVERT: C 95 LYS cc_start: 0.9417 (tttp) cc_final: 0.9194 (tptp) REVERT: C 101 THR cc_start: 0.9131 (m) cc_final: 0.8679 (p) REVERT: C 104 GLN cc_start: 0.8370 (mp-120) cc_final: 0.8070 (mp-120) REVERT: C 115 LEU cc_start: 0.9249 (mt) cc_final: 0.8991 (mt) REVERT: D 68 ASP cc_start: 0.9361 (t0) cc_final: 0.9025 (t0) REVERT: D 71 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8795 (tm-30) REVERT: D 79 ARG cc_start: 0.9365 (ttm-80) cc_final: 0.9123 (ttp-110) REVERT: D 88 THR cc_start: 0.9489 (m) cc_final: 0.9287 (p) REVERT: D 89 ILE cc_start: 0.9046 (mm) cc_final: 0.8765 (mm) REVERT: D 93 GLU cc_start: 0.9068 (pm20) cc_final: 0.8707 (pm20) REVERT: D 95 GLN cc_start: 0.9473 (tt0) cc_final: 0.9262 (tt0) REVERT: D 96 THR cc_start: 0.9563 (m) cc_final: 0.9322 (p) REVERT: E 50 GLU cc_start: 0.9410 (pt0) cc_final: 0.8787 (pt0) REVERT: E 90 MET cc_start: 0.8944 (mmp) cc_final: 0.8694 (mmm) REVERT: E 125 GLN cc_start: 0.9456 (mt0) cc_final: 0.9081 (mp10) REVERT: F 31 LYS cc_start: 0.9616 (tttp) cc_final: 0.9336 (tttm) REVERT: F 39 ARG cc_start: 0.9398 (mmt90) cc_final: 0.8775 (mmt90) REVERT: F 44 LYS cc_start: 0.9330 (tptm) cc_final: 0.9076 (tppp) REVERT: F 79 LYS cc_start: 0.9144 (mtpp) cc_final: 0.8780 (mtmm) REVERT: F 84 MET cc_start: 0.8831 (mmm) cc_final: 0.8445 (mmm) REVERT: F 95 ARG cc_start: 0.8883 (mtp85) cc_final: 0.8636 (mtt90) REVERT: G 32 ARG cc_start: 0.9285 (ttp80) cc_final: 0.9033 (ttp80) REVERT: G 38 ASN cc_start: 0.9287 (m-40) cc_final: 0.9044 (m-40) REVERT: G 39 TYR cc_start: 0.9460 (m-80) cc_final: 0.9239 (m-80) REVERT: G 42 ARG cc_start: 0.8877 (ptp-110) cc_final: 0.7826 (ptm-80) REVERT: G 61 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8922 (mm-30) REVERT: G 92 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8216 (tm-30) REVERT: H 37 TYR cc_start: 0.9373 (m-80) cc_final: 0.9075 (m-10) REVERT: H 68 ASP cc_start: 0.9345 (t0) cc_final: 0.8997 (t0) REVERT: H 83 TYR cc_start: 0.8923 (m-10) cc_final: 0.8628 (m-80) REVERT: H 84 ASN cc_start: 0.9185 (m110) cc_final: 0.8706 (m110) REVERT: H 86 ARG cc_start: 0.9375 (tpp80) cc_final: 0.8930 (tpp80) REVERT: H 92 ARG cc_start: 0.8880 (mtp-110) cc_final: 0.8312 (ttp80) REVERT: H 106 LEU cc_start: 0.9146 (mt) cc_final: 0.8896 (mt) REVERT: M 77 ASP cc_start: 0.8245 (m-30) cc_final: 0.7547 (p0) REVERT: M 104 MET cc_start: 0.9026 (mmm) cc_final: 0.8814 (mmm) REVERT: N 38 MET cc_start: 0.3624 (ppp) cc_final: 0.3245 (ppp) REVERT: N 79 ASN cc_start: 0.6364 (p0) cc_final: 0.6026 (p0) outliers start: 37 outliers final: 32 residues processed: 449 average time/residue: 0.1461 time to fit residues: 90.7310 Evaluate side-chains 444 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 412 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU 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 54 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR 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 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 64 ASN Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 LEU 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 61 VAL Chi-restraints excluded: chain N residue 31 PHE 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: 1.9990 chunk 110 optimal weight: 50.0000 chunk 56 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 120 optimal weight: 8.9990 chunk 99 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** 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** 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 = 0.3177 r_free = 0.3177 target = 0.050710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.040108 restraints weight = 93403.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.041349 restraints weight = 43008.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.042181 restraints weight = 25712.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.042731 restraints weight = 18112.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.043144 restraints weight = 14408.382| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 15436 Z= 0.202 Angle : 0.765 15.372 22114 Z= 0.415 Chirality : 0.046 0.269 2519 Planarity : 0.005 0.080 1788 Dihedral : 29.854 172.424 4403 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.95 % Rotamer: Outliers : 5.15 % Allowed : 24.32 % Favored : 70.54 % 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: 0.37 (0.25), residues: 1062 helix: 0.99 (0.20), residues: 664 sheet: 0.40 (1.21), residues: 24 loop : -1.07 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 39 TYR 0.034 0.002 TYR D 83 PHE 0.034 0.002 PHE E 67 TRP 0.006 0.001 TRP N 141 HIS 0.009 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.20 (15420) covalent geometry : angle 0.72941 / 0.41 (22096) hydrogen bonds : bond 0.05367 / 3.59 ( 872) hydrogen bonds : angle 3.88363 / 2.77 ( 2220) metal coordination : bond 0.02657 / 1.42 ( 16) metal coordination : angle 8.11008 / 4.61 ( 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 484 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 437 time to evaluate : 0.415 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: symmetry clash REVERT: A 85 GLN cc_start: 0.8863 (mt0) cc_final: 0.8640 (mt0) REVERT: A 94 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8663 (mm-30) REVERT: A 105 GLU cc_start: 0.8968 (tp30) cc_final: 0.8742 (tp30) REVERT: A 109 LEU cc_start: 0.9349 (mp) cc_final: 0.9008 (mt) REVERT: A 112 ILE cc_start: 0.9435 (pt) cc_final: 0.9139 (mt) REVERT: A 129 ARG cc_start: 0.8729 (tpm170) cc_final: 0.8471 (tpm170) REVERT: B 49 LEU cc_start: 0.9019 (mm) cc_final: 0.8468 (tp) REVERT: B 52 GLU cc_start: 0.8310 (pm20) cc_final: 0.7807 (pm20) REVERT: C 38 ASN cc_start: 0.8999 (m-40) cc_final: 0.8536 (p0) REVERT: C 68 ASN cc_start: 0.9372 (m-40) cc_final: 0.9131 (m110) REVERT: C 95 LYS cc_start: 0.9401 (tttp) cc_final: 0.9195 (tptp) REVERT: C 101 THR cc_start: 0.9092 (m) cc_final: 0.8636 (p) REVERT: C 104 GLN cc_start: 0.8370 (mp-120) cc_final: 0.8045 (mp-120) REVERT: D 40 TYR cc_start: 0.8757 (m-80) cc_final: 0.8462 (m-80) REVERT: D 68 ASP cc_start: 0.9372 (t0) cc_final: 0.9038 (t0) REVERT: D 71 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8794 (tm-30) REVERT: D 79 ARG cc_start: 0.9332 (ttm-80) cc_final: 0.9016 (ttp-110) REVERT: D 96 THR cc_start: 0.9583 (m) cc_final: 0.9284 (p) REVERT: E 50 GLU cc_start: 0.9386 (pt0) cc_final: 0.9130 (pt0) REVERT: E 90 MET cc_start: 0.8936 (mmp) cc_final: 0.8653 (mmm) REVERT: E 125 GLN cc_start: 0.9461 (mt0) cc_final: 0.9083 (mp10) REVERT: E 133 GLU cc_start: 0.8418 (mp0) cc_final: 0.8198 (mp0) REVERT: F 44 LYS cc_start: 0.9379 (tptm) cc_final: 0.8924 (mmmt) REVERT: F 84 MET cc_start: 0.8812 (mmm) cc_final: 0.8403 (mmm) REVERT: F 92 ARG cc_start: 0.9318 (mtp-110) cc_final: 0.9032 (ttt-90) REVERT: F 93 GLN cc_start: 0.8573 (mp10) cc_final: 0.8216 (mp10) REVERT: F 95 ARG cc_start: 0.8884 (mtp85) cc_final: 0.8623 (mtt90) REVERT: G 32 ARG cc_start: 0.9343 (ttp80) cc_final: 0.8841 (ttp80) REVERT: G 36 LYS cc_start: 0.9177 (mmtm) cc_final: 0.8715 (mmtm) REVERT: G 38 ASN cc_start: 0.9242 (m-40) cc_final: 0.8996 (m-40) REVERT: G 39 TYR cc_start: 0.9457 (m-80) cc_final: 0.9218 (m-80) REVERT: G 42 ARG cc_start: 0.8900 (ptp-110) cc_final: 0.8101 (ptm160) REVERT: G 81 ARG cc_start: 0.9146 (tpt170) cc_final: 0.8832 (tpt170) REVERT: H 37 TYR cc_start: 0.9347 (m-80) cc_final: 0.8894 (m-80) REVERT: H 42 TYR cc_start: 0.8844 (t80) cc_final: 0.8579 (t80) REVERT: H 68 ASP cc_start: 0.9256 (t0) cc_final: 0.8133 (t0) REVERT: H 72 ARG cc_start: 0.9365 (ttm170) cc_final: 0.8896 (ttm170) REVERT: H 84 ASN cc_start: 0.9159 (m110) cc_final: 0.8676 (m110) REVERT: H 86 ARG cc_start: 0.9384 (tpp80) cc_final: 0.8965 (tpp80) REVERT: M 77 ASP cc_start: 0.8209 (m-30) cc_final: 0.7536 (p0) REVERT: M 104 MET cc_start: 0.9068 (mmm) cc_final: 0.8852 (mmm) REVERT: N 38 MET cc_start: 0.3627 (ppp) cc_final: 0.3256 (ppp) REVERT: N 79 ASN cc_start: 0.6537 (p0) cc_final: 0.6185 (p0) outliers start: 47 outliers final: 33 residues processed: 453 average time/residue: 0.1484 time to fit residues: 93.3291 Evaluate side-chains 450 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 416 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 64 GLU Chi-restraints excluded: chain C residue 76 THR 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 71 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 94 ILE 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 E residue 118 THR 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 F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 97 LEU 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 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: 0.6980 chunk 106 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 121 optimal weight: 0.0670 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 2 optimal weight: 0.0770 chunk 108 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN C 82 HIS E 68 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 HIS ** 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 = 0.3214 r_free = 0.3214 target = 0.052172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.041537 restraints weight = 93770.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.042780 restraints weight = 43483.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.043538 restraints weight = 26290.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.044145 restraints weight = 19179.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.044543 restraints weight = 15177.551| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 15436 Z= 0.158 Angle : 0.758 13.577 22114 Z= 0.409 Chirality : 0.046 0.393 2519 Planarity : 0.005 0.057 1788 Dihedral : 29.844 173.185 4403 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.14 % Rotamer: Outliers : 4.38 % Allowed : 27.82 % Favored : 67.80 % 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: 0.35 (0.25), residues: 1062 helix: 0.93 (0.20), residues: 663 sheet: 0.46 (1.20), residues: 24 loop : -0.96 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 39 TYR 0.019 0.002 TYR N 60 PHE 0.023 0.002 PHE F 61 TRP 0.006 0.001 TRP N 141 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 (15420) covalent geometry : angle 0.72901 / 0.41 (22096) hydrogen bonds : bond 0.04597 / 3.10 ( 872) hydrogen bonds : angle 3.72731 / 2.65 ( 2220) metal coordination : bond 0.02724 / 1.38 ( 16) metal coordination : angle 7.27394 / 4.16 ( 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 493 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 453 time to evaluate : 0.433 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 80 THR cc_start: 0.9436 (p) cc_final: 0.9203 (p) REVERT: A 129 ARG cc_start: 0.8764 (tpm170) cc_final: 0.8450 (tpm170) REVERT: B 39 ARG cc_start: 0.9229 (mmt180) cc_final: 0.8639 (mmt180) REVERT: B 49 LEU cc_start: 0.9024 (mm) cc_final: 0.8792 (tp) REVERT: B 53 GLU cc_start: 0.8290 (pm20) cc_final: 0.7981 (pm20) REVERT: B 67 ARG cc_start: 0.8788 (ttm110) cc_final: 0.8537 (ttm110) REVERT: B 79 LYS cc_start: 0.9082 (mtmt) cc_final: 0.8675 (ptpt) REVERT: C 38 ASN cc_start: 0.8884 (m-40) cc_final: 0.8544 (p0) REVERT: C 39 TYR cc_start: 0.9352 (m-80) cc_final: 0.9117 (m-80) REVERT: C 75 LYS cc_start: 0.8648 (mmmm) cc_final: 0.8426 (mmmm) REVERT: C 90 ASP cc_start: 0.8880 (t0) cc_final: 0.8388 (t0) REVERT: C 101 THR cc_start: 0.9018 (m) cc_final: 0.8523 (p) REVERT: C 104 GLN cc_start: 0.8386 (mp-120) cc_final: 0.8094 (mp10) REVERT: D 47 GLN cc_start: 0.9245 (tm-30) cc_final: 0.8929 (tm-30) REVERT: D 59 MET cc_start: 0.9625 (tpt) cc_final: 0.9410 (tpt) REVERT: D 68 ASP cc_start: 0.9384 (t0) cc_final: 0.9123 (t0) REVERT: D 71 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8698 (tm-30) REVERT: D 96 THR cc_start: 0.9578 (m) cc_final: 0.9347 (p) REVERT: E 50 GLU cc_start: 0.9358 (pt0) cc_final: 0.9141 (pt0) REVERT: E 122 LYS cc_start: 0.9194 (ptmt) cc_final: 0.8717 (ptmt) REVERT: E 125 GLN cc_start: 0.9449 (mt0) cc_final: 0.9048 (mp10) REVERT: E 133 GLU cc_start: 0.8451 (mp0) cc_final: 0.8219 (mp0) REVERT: F 44 LYS cc_start: 0.9422 (tptm) cc_final: 0.9019 (tppp) REVERT: F 79 LYS cc_start: 0.9092 (mtpp) cc_final: 0.8741 (mtmm) REVERT: F 84 MET cc_start: 0.8747 (mmm) cc_final: 0.8156 (mmm) REVERT: F 92 ARG cc_start: 0.9295 (mtp-110) cc_final: 0.8773 (ttt-90) REVERT: F 95 ARG cc_start: 0.8842 (mtp85) cc_final: 0.8508 (mtt90) REVERT: G 32 ARG cc_start: 0.9327 (ttp80) cc_final: 0.8849 (tmm-80) REVERT: G 35 ARG cc_start: 0.8819 (mtm110) cc_final: 0.8446 (mtp-110) REVERT: G 36 LYS cc_start: 0.9177 (mmtm) cc_final: 0.8282 (mmtm) REVERT: G 38 ASN cc_start: 0.9210 (m-40) cc_final: 0.8933 (m-40) REVERT: G 39 TYR cc_start: 0.9465 (m-80) cc_final: 0.9168 (m-80) REVERT: G 42 ARG cc_start: 0.8850 (ptp-110) cc_final: 0.8097 (ptm160) REVERT: G 81 ARG cc_start: 0.9088 (tpt170) cc_final: 0.8885 (tpt170) REVERT: G 90 ASP cc_start: 0.8458 (t0) cc_final: 0.8100 (t0) REVERT: H 37 TYR cc_start: 0.9344 (m-80) cc_final: 0.8996 (m-80) REVERT: H 42 TYR cc_start: 0.8794 (t80) cc_final: 0.8500 (t80) REVERT: H 68 ASP cc_start: 0.9271 (t0) cc_final: 0.8372 (t0) REVERT: H 70 PHE cc_start: 0.9402 (t80) cc_final: 0.9152 (t80) REVERT: H 72 ARG cc_start: 0.9367 (ttm170) cc_final: 0.9059 (ttm170) REVERT: H 84 ASN cc_start: 0.9111 (m-40) cc_final: 0.8557 (m-40) REVERT: H 86 ARG cc_start: 0.9354 (tpp80) cc_final: 0.8882 (tpp80) REVERT: H 92 ARG cc_start: 0.8812 (mtp-110) cc_final: 0.8103 (ttp80) REVERT: K 33 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7020 (pm20) REVERT: K 43 PHE cc_start: 0.7761 (m-10) cc_final: 0.7415 (m-80) REVERT: N 38 MET cc_start: 0.3704 (ppp) cc_final: 0.3376 (ppp) REVERT: N 79 ASN cc_start: 0.6504 (p0) cc_final: 0.6116 (p0) REVERT: N 140 GLU cc_start: 0.9223 (pt0) cc_final: 0.9012 (pt0) outliers start: 40 outliers final: 29 residues processed: 466 average time/residue: 0.1536 time to fit residues: 98.5100 Evaluate side-chains 441 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 410 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASN 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 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 88 THR 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 F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 103 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 64 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 89 optimal weight: 30.0000 chunk 73 optimal weight: 30.0000 chunk 11 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN C 94 ASN E 108 ASN ** G 73 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.051567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.041046 restraints weight = 94102.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.042263 restraints weight = 43502.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.043051 restraints weight = 26182.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.043621 restraints weight = 18801.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.044065 restraints weight = 14890.165| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 15436 Z= 0.179 Angle : 0.783 15.084 22114 Z= 0.417 Chirality : 0.046 0.329 2519 Planarity : 0.005 0.068 1788 Dihedral : 29.907 173.331 4403 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.95 % Rotamer: Outliers : 5.91 % Allowed : 29.03 % Favored : 65.06 % 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: 0.29 (0.25), residues: 1062 helix: 0.86 (0.20), residues: 663 sheet: 0.45 (1.19), residues: 24 loop : -0.94 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 92 TYR 0.054 0.002 TYR H 83 PHE 0.023 0.002 PHE B 61 TRP 0.005 0.001 TRP N 141 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 (15420) covalent geometry : angle 0.75362 / 0.42 (22096) hydrogen bonds : bond 0.04865 / 3.26 ( 872) hydrogen bonds : angle 3.77851 / 2.69 ( 2220) metal coordination : bond 0.02401 / 1.25 ( 16) metal coordination : angle 7.45712 / 4.14 ( 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 473 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 419 time to evaluate : 0.431 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 93 GLN cc_start: 0.8602 (tp40) cc_final: 0.7992 (tp40) REVERT: A 97 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: A 129 ARG cc_start: 0.8783 (tpm170) cc_final: 0.8440 (tpm170) REVERT: B 52 GLU cc_start: 0.8310 (pm20) cc_final: 0.7980 (pm20) REVERT: B 79 LYS cc_start: 0.9046 (mtmt) cc_final: 0.8668 (ptpt) REVERT: C 38 ASN cc_start: 0.8932 (m-40) cc_final: 0.8589 (p0) REVERT: C 39 TYR cc_start: 0.9363 (m-80) cc_final: 0.9143 (m-80) REVERT: C 68 ASN cc_start: 0.8982 (m-40) cc_final: 0.8697 (m110) REVERT: C 90 ASP cc_start: 0.8684 (t0) cc_final: 0.8404 (t0) REVERT: C 101 THR cc_start: 0.8993 (m) cc_final: 0.8479 (p) REVERT: C 104 GLN cc_start: 0.8436 (mp-120) cc_final: 0.8069 (mp-120) REVERT: D 47 GLN cc_start: 0.9319 (tm-30) cc_final: 0.8967 (tm-30) REVERT: D 68 ASP cc_start: 0.9422 (t0) cc_final: 0.9115 (t0) REVERT: D 71 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8703 (tm-30) REVERT: D 93 GLU cc_start: 0.9192 (pm20) cc_final: 0.8919 (pm20) REVERT: D 95 GLN cc_start: 0.9520 (tt0) cc_final: 0.9299 (tt0) REVERT: D 96 THR cc_start: 0.9567 (m) cc_final: 0.9328 (p) REVERT: D 105 GLU cc_start: 0.8537 (pm20) cc_final: 0.8096 (pm20) REVERT: D 108 LYS cc_start: 0.9312 (ptpp) cc_final: 0.9077 (pttp) REVERT: D 120 LYS cc_start: 0.9336 (tttp) cc_final: 0.9088 (ttpp) REVERT: E 50 GLU cc_start: 0.9355 (pt0) cc_final: 0.9111 (pt0) REVERT: E 79 LYS cc_start: 0.9226 (tptm) cc_final: 0.8843 (tptp) REVERT: E 122 LYS cc_start: 0.9223 (ptmt) cc_final: 0.8768 (ptmt) REVERT: E 125 GLN cc_start: 0.9463 (mt0) cc_final: 0.9058 (mp10) REVERT: E 133 GLU cc_start: 0.8479 (mp0) cc_final: 0.8233 (mp0) REVERT: F 44 LYS cc_start: 0.9432 (tptm) cc_final: 0.9120 (tppp) REVERT: F 84 MET cc_start: 0.8673 (mmm) cc_final: 0.8075 (mmm) REVERT: F 93 GLN cc_start: 0.8737 (mp10) cc_final: 0.8316 (mp10) REVERT: F 95 ARG cc_start: 0.8811 (mtp85) cc_final: 0.8529 (mtt90) REVERT: G 32 ARG cc_start: 0.9361 (ttp80) cc_final: 0.8657 (ttp80) REVERT: G 35 ARG cc_start: 0.8839 (mtm110) cc_final: 0.8392 (mtp-110) REVERT: G 36 LYS cc_start: 0.9187 (mmtm) cc_final: 0.8248 (mmtm) REVERT: G 38 ASN cc_start: 0.9195 (m-40) cc_final: 0.8931 (m-40) REVERT: G 39 TYR cc_start: 0.9424 (m-80) cc_final: 0.9181 (m-80) REVERT: G 42 ARG cc_start: 0.8875 (ptp-110) cc_final: 0.8114 (ptm160) REVERT: H 33 ARG cc_start: 0.8314 (mmm160) cc_final: 0.7992 (mmm160) REVERT: H 37 TYR cc_start: 0.9369 (m-80) cc_final: 0.9049 (m-80) REVERT: H 42 TYR cc_start: 0.8849 (t80) cc_final: 0.8594 (t80) REVERT: H 68 ASP cc_start: 0.9281 (t0) cc_final: 0.8334 (t0) REVERT: H 70 PHE cc_start: 0.9410 (t80) cc_final: 0.9110 (t80) REVERT: H 72 ARG cc_start: 0.9389 (ttm170) cc_final: 0.9063 (ttm170) REVERT: H 84 ASN cc_start: 0.9156 (m-40) cc_final: 0.8573 (m-40) REVERT: H 86 ARG cc_start: 0.9357 (tpp80) cc_final: 0.8849 (tpp80) REVERT: H 92 ARG cc_start: 0.8789 (mtp-110) cc_final: 0.8044 (ttp80) REVERT: K 33 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7073 (pm20) REVERT: M 104 MET cc_start: 0.8876 (mmm) cc_final: 0.8535 (mmt) REVERT: N 38 MET cc_start: 0.4105 (ppp) cc_final: 0.3727 (ppp) REVERT: N 79 ASN cc_start: 0.6480 (p0) cc_final: 0.6060 (p0) REVERT: N 140 GLU cc_start: 0.9195 (pt0) cc_final: 0.8896 (pt0) REVERT: N 143 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8550 (mm-40) outliers start: 54 outliers final: 37 residues processed: 443 average time/residue: 0.1495 time to fit residues: 91.5258 Evaluate side-chains 441 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 400 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 25 ASN 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 64 ASN 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 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU 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 71 GLU Chi-restraints excluded: chain D residue 88 THR 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 F residue 82 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 GLU 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 94 ILE Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 106 ILE 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: 7.9990 chunk 50 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN G 31 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.050761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.040210 restraints weight = 94547.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.041428 restraints weight = 43438.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.042211 restraints weight = 26091.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.042819 restraints weight = 18641.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.043244 restraints weight = 14485.358| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 15436 Z= 0.215 Angle : 0.808 15.844 22114 Z= 0.431 Chirality : 0.046 0.357 2519 Planarity : 0.005 0.072 1788 Dihedral : 30.061 173.326 4403 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 4.93 % Allowed : 31.54 % Favored : 63.53 % 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: 0.87 (0.20), residues: 663 sheet: 0.45 (1.20), residues: 24 loop : -0.98 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 112 TYR 0.030 0.002 TYR H 83 PHE 0.025 0.002 PHE F 61 TRP 0.004 0.001 TRP N 141 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.21 (15420) covalent geometry : angle 0.78014 / 0.43 (22096) hydrogen bonds : bond 0.05367 / 3.57 ( 872) hydrogen bonds : angle 3.88477 / 2.77 ( 2220) metal coordination : bond 0.02304 / 1.22 ( 16) metal coordination : angle 7.45279 / 4.03 ( 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 460 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 415 time to evaluate : 0.332 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: A 85 GLN cc_start: 0.8802 (mt0) cc_final: 0.8407 (mp10) REVERT: A 93 GLN cc_start: 0.8628 (tp40) cc_final: 0.8104 (tp40) REVERT: A 94 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8699 (mm-30) REVERT: A 112 ILE cc_start: 0.9481 (pt) cc_final: 0.9188 (mt) REVERT: A 129 ARG cc_start: 0.8805 (tpm170) cc_final: 0.8447 (tpm170) REVERT: B 31 LYS cc_start: 0.9181 (ttmm) cc_final: 0.8829 (ttmm) REVERT: B 79 LYS cc_start: 0.9107 (mtmt) cc_final: 0.8678 (ptpt) REVERT: B 98 TYR cc_start: 0.9066 (m-10) cc_final: 0.8787 (m-10) REVERT: C 38 ASN cc_start: 0.8944 (m-40) cc_final: 0.8541 (p0) REVERT: C 90 ASP cc_start: 0.8599 (t0) cc_final: 0.8270 (t0) REVERT: C 101 THR cc_start: 0.8944 (m) cc_final: 0.8399 (p) REVERT: D 47 GLN cc_start: 0.9342 (tm-30) cc_final: 0.8941 (tm-30) REVERT: D 68 ASP cc_start: 0.9444 (t0) cc_final: 0.9147 (t0) REVERT: D 71 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8820 (tm-30) REVERT: D 95 GLN cc_start: 0.9530 (tt0) cc_final: 0.9294 (tt0) REVERT: D 96 THR cc_start: 0.9556 (m) cc_final: 0.9307 (p) REVERT: D 105 GLU cc_start: 0.8551 (pm20) cc_final: 0.8070 (pm20) REVERT: D 108 LYS cc_start: 0.9340 (ptpp) cc_final: 0.9093 (pttp) REVERT: D 120 LYS cc_start: 0.9344 (tttp) cc_final: 0.9068 (tttp) REVERT: E 125 GLN cc_start: 0.9494 (mt0) cc_final: 0.9137 (mp10) REVERT: E 133 GLU cc_start: 0.8535 (mp0) cc_final: 0.8229 (mp0) REVERT: F 44 LYS cc_start: 0.9418 (tptm) cc_final: 0.9110 (tppp) REVERT: F 59 LYS cc_start: 0.9527 (ptmm) cc_final: 0.9137 (ptmm) REVERT: F 63 GLU cc_start: 0.9334 (pm20) cc_final: 0.9048 (pm20) REVERT: F 84 MET cc_start: 0.8725 (mmm) cc_final: 0.7394 (mmm) REVERT: F 88 TYR cc_start: 0.8911 (m-10) cc_final: 0.7587 (m-80) REVERT: F 95 ARG cc_start: 0.8842 (mtp85) cc_final: 0.8561 (mtt90) REVERT: G 32 ARG cc_start: 0.9402 (ttp80) cc_final: 0.8834 (tmm-80) REVERT: G 36 LYS cc_start: 0.9198 (mmtm) cc_final: 0.8710 (mmtm) REVERT: G 38 ASN cc_start: 0.9239 (m-40) cc_final: 0.8953 (m-40) REVERT: G 39 TYR cc_start: 0.9423 (m-80) cc_final: 0.9181 (m-80) REVERT: G 42 ARG cc_start: 0.8895 (ptp-110) cc_final: 0.8126 (ptm160) REVERT: H 33 ARG cc_start: 0.8407 (mmm160) cc_final: 0.7621 (tpp80) REVERT: H 37 TYR cc_start: 0.9416 (m-80) cc_final: 0.9098 (m-80) REVERT: H 42 TYR cc_start: 0.8883 (t80) cc_final: 0.8626 (t80) REVERT: H 68 ASP cc_start: 0.9310 (t70) cc_final: 0.8922 (t0) REVERT: H 70 PHE cc_start: 0.9393 (t80) cc_final: 0.9160 (t80) REVERT: H 84 ASN cc_start: 0.9136 (m-40) cc_final: 0.8546 (m-40) REVERT: H 86 ARG cc_start: 0.9373 (tpp80) cc_final: 0.8815 (tpp80) REVERT: H 92 ARG cc_start: 0.8842 (mtp-110) cc_final: 0.8466 (ttp-110) REVERT: K 43 PHE cc_start: 0.8088 (m-10) cc_final: 0.7635 (m-80) REVERT: M 104 MET cc_start: 0.9001 (mmm) cc_final: 0.8745 (mmm) REVERT: N 38 MET cc_start: 0.3534 (ppp) cc_final: 0.3180 (ppp) REVERT: N 79 ASN cc_start: 0.6556 (p0) cc_final: 0.6161 (p0) REVERT: N 140 GLU cc_start: 0.9203 (pt0) cc_final: 0.8903 (pt0) REVERT: N 143 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8521 (mm-40) outliers start: 45 outliers final: 33 residues processed: 430 average time/residue: 0.1473 time to fit residues: 87.9818 Evaluate side-chains 439 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 404 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 64 ASN 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 93 LEU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 46 VAL 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 F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 GLU 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 94 ILE Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 101 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 111 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 118 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN C 104 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.051816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.041333 restraints weight = 92810.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.042519 restraints weight = 43262.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.043258 restraints weight = 26301.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.043876 restraints weight = 19264.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.044202 restraints weight = 15017.188| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 15436 Z= 0.162 Angle : 0.810 17.322 22114 Z= 0.426 Chirality : 0.046 0.390 2519 Planarity : 0.005 0.055 1788 Dihedral : 30.046 173.810 4403 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.95 % Rotamer: Outliers : 4.60 % Allowed : 32.97 % Favored : 62.43 % 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: 0.30 (0.26), residues: 1062 helix: 0.87 (0.20), residues: 663 sheet: 0.47 (1.19), residues: 24 loop : -0.94 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 112 TYR 0.022 0.002 TYR G 57 PHE 0.025 0.002 PHE F 61 TRP 0.005 0.001 TRP N 141 HIS 0.005 0.001 HIS K 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (15420) covalent geometry : angle 0.78523 / 0.42 (22096) hydrogen bonds : bond 0.04630 / 3.14 ( 872) hydrogen bonds : angle 3.73160 / 2.64 ( 2220) metal coordination : bond 0.02556 / 1.28 ( 16) metal coordination : angle 7.06989 / 3.83 ( 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 472 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 430 time to evaluate : 0.378 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 85 GLN cc_start: 0.8672 (mt0) cc_final: 0.8388 (mp10) REVERT: A 94 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8449 (mt-10) REVERT: A 112 ILE cc_start: 0.9427 (pt) cc_final: 0.9169 (mt) REVERT: A 129 ARG cc_start: 0.8788 (tpm170) cc_final: 0.8419 (tpm170) REVERT: C 38 ASN cc_start: 0.8803 (m-40) cc_final: 0.8523 (p0) REVERT: C 39 TYR cc_start: 0.9362 (m-80) cc_final: 0.9140 (m-80) REVERT: C 75 LYS cc_start: 0.8569 (mmmm) cc_final: 0.8289 (mmmm) REVERT: C 90 ASP cc_start: 0.8648 (t0) cc_final: 0.8402 (t0) REVERT: C 101 THR cc_start: 0.8930 (m) cc_final: 0.8417 (p) REVERT: D 47 GLN cc_start: 0.9313 (tm-30) cc_final: 0.8936 (tm-30) REVERT: D 59 MET cc_start: 0.9652 (tpt) cc_final: 0.9319 (tpt) REVERT: D 68 ASP cc_start: 0.9414 (t0) cc_final: 0.9183 (t0) REVERT: D 71 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8645 (tm-30) REVERT: D 93 GLU cc_start: 0.9078 (pm20) cc_final: 0.8803 (pm20) REVERT: D 96 THR cc_start: 0.9549 (m) cc_final: 0.9336 (p) REVERT: D 120 LYS cc_start: 0.9350 (tttp) cc_final: 0.9070 (ttpp) REVERT: E 120 MET cc_start: 0.8555 (mmm) cc_final: 0.8305 (mmm) REVERT: E 122 LYS cc_start: 0.9167 (ptmt) cc_final: 0.8738 (ptmt) REVERT: E 125 GLN cc_start: 0.9471 (mt0) cc_final: 0.9096 (mp10) REVERT: E 133 GLU cc_start: 0.8557 (mp0) cc_final: 0.8249 (mp0) REVERT: F 30 THR cc_start: 0.9164 (p) cc_final: 0.8949 (t) REVERT: F 44 LYS cc_start: 0.9395 (tptm) cc_final: 0.9135 (tppp) REVERT: F 79 LYS cc_start: 0.9056 (mtpp) cc_final: 0.8691 (mtmm) REVERT: F 84 MET cc_start: 0.8560 (mmm) cc_final: 0.7213 (mmm) REVERT: F 88 TYR cc_start: 0.8669 (m-10) cc_final: 0.7421 (m-80) REVERT: F 92 ARG cc_start: 0.9337 (mtp-110) cc_final: 0.8978 (ttt-90) REVERT: F 95 ARG cc_start: 0.8785 (mtp85) cc_final: 0.8529 (mtt90) REVERT: G 32 ARG cc_start: 0.9361 (ttp80) cc_final: 0.8817 (tmm-80) REVERT: G 36 LYS cc_start: 0.9218 (mmtm) cc_final: 0.8728 (mmtm) REVERT: G 38 ASN cc_start: 0.9203 (m-40) cc_final: 0.8902 (m-40) REVERT: G 39 TYR cc_start: 0.9406 (m-80) cc_final: 0.9079 (m-80) REVERT: G 42 ARG cc_start: 0.8852 (ptp-110) cc_final: 0.8089 (ptm160) REVERT: G 57 TYR cc_start: 0.9195 (t80) cc_final: 0.8408 (t80) REVERT: G 61 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8246 (mp0) REVERT: G 75 LYS cc_start: 0.9381 (mmtt) cc_final: 0.9049 (mmtm) REVERT: H 33 ARG cc_start: 0.8285 (mmm160) cc_final: 0.7773 (tpt170) REVERT: H 37 TYR cc_start: 0.9331 (m-80) cc_final: 0.9033 (m-80) REVERT: H 42 TYR cc_start: 0.8765 (t80) cc_final: 0.8476 (t80) REVERT: H 68 ASP cc_start: 0.9245 (t70) cc_final: 0.8561 (t0) REVERT: H 70 PHE cc_start: 0.9421 (t80) cc_final: 0.9151 (t80) REVERT: H 84 ASN cc_start: 0.9143 (m-40) cc_final: 0.8606 (m-40) REVERT: H 86 ARG cc_start: 0.9349 (tpp80) cc_final: 0.8965 (tpp80) REVERT: H 92 ARG cc_start: 0.8797 (mtp-110) cc_final: 0.8120 (ttp80) REVERT: N 38 MET cc_start: 0.3696 (ppp) cc_final: 0.3373 (ppp) REVERT: N 79 ASN cc_start: 0.6480 (p0) cc_final: 0.6056 (p0) REVERT: N 140 GLU cc_start: 0.9196 (pt0) cc_final: 0.8907 (pt0) REVERT: N 143 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8526 (mm-40) outliers start: 42 outliers final: 29 residues processed: 446 average time/residue: 0.1467 time to fit residues: 91.1538 Evaluate side-chains 437 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 406 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 64 ASN 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 62 ILE Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 88 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 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 LEU 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 88 THR Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 101 LEU 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: 9.9990 chunk 18 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 89 optimal weight: 30.0000 chunk 46 optimal weight: 0.0570 chunk 32 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN E 93 GLN E 108 ASN ** 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 = 0.3220 r_free = 0.3220 target = 0.052426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.041971 restraints weight = 93547.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.043205 restraints weight = 43291.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.044023 restraints weight = 25811.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.044589 restraints weight = 18355.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.044961 restraints weight = 14556.771| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 15436 Z= 0.163 Angle : 0.840 17.524 22114 Z= 0.441 Chirality : 0.048 0.429 2519 Planarity : 0.005 0.060 1788 Dihedral : 30.009 174.424 4403 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.95 % Rotamer: Outliers : 3.50 % Allowed : 34.94 % Favored : 61.56 % Cbeta Deviations : 0.10 % 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: 0.80 (0.20), residues: 660 sheet: 0.56 (1.20), residues: 24 loop : -0.93 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 112 TYR 0.016 0.001 TYR G 57 PHE 0.051 0.002 PHE A 67 TRP 0.004 0.001 TRP N 141 HIS 0.005 0.001 HIS K 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (15420) covalent geometry : angle 0.81918 / 0.44 (22096) hydrogen bonds : bond 0.04590 / 3.14 ( 872) hydrogen bonds : angle 3.81070 / 2.69 ( 2220) metal coordination : bond 0.02405 / 1.20 ( 16) metal coordination : angle 6.63051 / 3.48 ( 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 477 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 445 time to evaluate : 0.431 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: symmetry clash REVERT: A 41 TYR cc_start: 0.8472 (m-80) cc_final: 0.7952 (m-80) REVERT: A 85 GLN cc_start: 0.8578 (mt0) cc_final: 0.8289 (mp10) REVERT: A 94 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8360 (mt-10) REVERT: A 129 ARG cc_start: 0.8809 (tpm170) cc_final: 0.8434 (tpm170) REVERT: B 31 LYS cc_start: 0.9182 (ttpp) cc_final: 0.8921 (ttmm) REVERT: B 35 ARG cc_start: 0.9286 (ttm110) cc_final: 0.8788 (ttm110) REVERT: C 38 ASN cc_start: 0.8854 (m-40) cc_final: 0.8551 (p0) REVERT: C 39 TYR cc_start: 0.9335 (m-80) cc_final: 0.9112 (m-80) REVERT: C 75 LYS cc_start: 0.8530 (mmmm) cc_final: 0.8226 (mmmm) REVERT: C 90 ASP cc_start: 0.8729 (t0) cc_final: 0.8121 (t70) REVERT: C 101 THR cc_start: 0.8895 (m) cc_final: 0.8367 (p) REVERT: D 33 ARG cc_start: 0.8688 (ttt90) cc_final: 0.8473 (tpt-90) REVERT: D 47 GLN cc_start: 0.9325 (tm-30) cc_final: 0.8933 (tm-30) REVERT: D 71 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8673 (tm-30) REVERT: D 93 GLU cc_start: 0.9052 (pm20) cc_final: 0.8389 (pm20) REVERT: D 96 THR cc_start: 0.9545 (m) cc_final: 0.9329 (p) REVERT: D 105 GLU cc_start: 0.8409 (pm20) cc_final: 0.6951 (tt0) REVERT: D 108 LYS cc_start: 0.9262 (ptpp) cc_final: 0.8993 (pttp) REVERT: D 120 LYS cc_start: 0.9372 (tttp) cc_final: 0.9096 (ttpp) REVERT: E 120 MET cc_start: 0.8580 (mmm) cc_final: 0.8310 (mmm) REVERT: E 122 LYS cc_start: 0.9177 (ptmt) cc_final: 0.8540 (ptmm) REVERT: E 125 GLN cc_start: 0.9467 (mt0) cc_final: 0.9065 (mp10) REVERT: E 133 GLU cc_start: 0.8591 (mp0) cc_final: 0.8268 (mp0) REVERT: F 44 LYS cc_start: 0.9376 (tptm) cc_final: 0.9118 (tppp) REVERT: F 78 ARG cc_start: 0.8512 (ttp80) cc_final: 0.8126 (ttp80) REVERT: F 79 LYS cc_start: 0.9032 (mtpp) cc_final: 0.8657 (mtmm) REVERT: F 84 MET cc_start: 0.8559 (mmm) cc_final: 0.7474 (mmm) REVERT: F 88 TYR cc_start: 0.8586 (m-10) cc_final: 0.7275 (m-80) REVERT: F 92 ARG cc_start: 0.9337 (mtp-110) cc_final: 0.8993 (ttt-90) REVERT: F 95 ARG cc_start: 0.8756 (mtp85) cc_final: 0.8479 (mtt90) REVERT: G 32 ARG cc_start: 0.9357 (ttp80) cc_final: 0.8778 (tmm-80) REVERT: G 36 LYS cc_start: 0.9220 (mmtm) cc_final: 0.8779 (mmtm) REVERT: G 38 ASN cc_start: 0.9138 (m-40) cc_final: 0.8834 (m-40) REVERT: G 39 TYR cc_start: 0.9391 (m-80) cc_final: 0.8991 (m-80) REVERT: G 42 ARG cc_start: 0.8854 (ptp-110) cc_final: 0.8154 (ptm-80) REVERT: G 57 TYR cc_start: 0.9195 (t80) cc_final: 0.8339 (t80) REVERT: G 61 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8351 (mp0) REVERT: G 75 LYS cc_start: 0.9323 (mmtt) cc_final: 0.9019 (mmtm) REVERT: G 90 ASP cc_start: 0.8575 (t0) cc_final: 0.8355 (t0) REVERT: H 33 ARG cc_start: 0.8305 (mmm160) cc_final: 0.7659 (tpp80) REVERT: H 37 TYR cc_start: 0.9309 (m-80) cc_final: 0.8974 (m-80) REVERT: H 40 TYR cc_start: 0.9325 (m-80) cc_final: 0.8857 (m-80) REVERT: H 42 TYR cc_start: 0.8791 (t80) cc_final: 0.8501 (t80) REVERT: H 70 PHE cc_start: 0.9363 (t80) cc_final: 0.9127 (t80) REVERT: H 84 ASN cc_start: 0.9093 (m-40) cc_final: 0.8570 (m-40) REVERT: H 86 ARG cc_start: 0.9365 (tpp80) cc_final: 0.8976 (tpp80) REVERT: H 92 ARG cc_start: 0.8770 (mtp-110) cc_final: 0.8316 (ttp80) REVERT: N 29 ASP cc_start: 0.6457 (t70) cc_final: 0.5944 (p0) REVERT: N 38 MET cc_start: 0.3892 (ppp) cc_final: 0.3576 (ppp) REVERT: N 79 ASN cc_start: 0.6518 (p0) cc_final: 0.6089 (p0) REVERT: N 140 GLU cc_start: 0.9190 (pt0) cc_final: 0.8891 (pt0) REVERT: N 143 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8548 (mm-40) outliers start: 32 outliers final: 23 residues processed: 458 average time/residue: 0.1518 time to fit residues: 95.7810 Evaluate side-chains 435 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 410 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU 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 D residue 55 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 88 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 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 97 LEU 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 88 THR Chi-restraints excluded: chain K residue 73 LEU 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: 7.9990 chunk 93 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 120 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN 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 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** N 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.051321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.040944 restraints weight = 94016.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.042160 restraints weight = 43615.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.042977 restraints weight = 26024.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.043492 restraints weight = 18318.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.043924 restraints weight = 14608.191| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 15436 Z= 0.199 Angle : 0.872 18.854 22114 Z= 0.455 Chirality : 0.050 0.424 2519 Planarity : 0.005 0.062 1788 Dihedral : 30.131 174.318 4403 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.76 % Rotamer: Outliers : 3.07 % Allowed : 35.93 % Favored : 61.01 % 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: 0.18 (0.25), residues: 1062 helix: 0.75 (0.20), residues: 662 sheet: 0.64 (1.20), residues: 24 loop : -0.95 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 112 TYR 0.018 0.002 TYR N 60 PHE 0.057 0.003 PHE A 67 TRP 0.003 0.001 TRP N 141 HIS 0.004 0.001 HIS K 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 (15420) covalent geometry : angle 0.85012 / 0.45 (22096) hydrogen bonds : bond 0.05162 / 3.51 ( 872) hydrogen bonds : angle 3.99623 / 2.82 ( 2220) metal coordination : bond 0.02391 / 1.23 ( 16) metal coordination : angle 6.91751 / 3.52 ( 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 438 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 410 time to evaluate : 0.460 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: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.8495 (m-80) cc_final: 0.7977 (m-80) REVERT: A 112 ILE cc_start: 0.9455 (pt) cc_final: 0.9188 (mt) REVERT: A 129 ARG cc_start: 0.8825 (tpm170) cc_final: 0.8441 (tpm170) REVERT: C 38 ASN cc_start: 0.8770 (m-40) cc_final: 0.8570 (p0) REVERT: C 39 TYR cc_start: 0.9363 (m-80) cc_final: 0.9156 (m-80) REVERT: C 56 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8911 (mt-10) REVERT: C 75 LYS cc_start: 0.8576 (mmmm) cc_final: 0.8257 (mmmm) REVERT: C 90 ASP cc_start: 0.8705 (t0) cc_final: 0.8325 (t70) REVERT: C 101 THR cc_start: 0.8869 (m) cc_final: 0.8363 (p) REVERT: D 47 GLN cc_start: 0.9302 (tm-30) cc_final: 0.8932 (tm-30) REVERT: D 68 ASP cc_start: 0.9397 (t0) cc_final: 0.9084 (t0) REVERT: D 71 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8654 (tm-30) REVERT: D 93 GLU cc_start: 0.9078 (pm20) cc_final: 0.8819 (pm20) REVERT: D 96 THR cc_start: 0.9578 (m) cc_final: 0.9364 (p) REVERT: D 108 LYS cc_start: 0.9294 (ptpp) cc_final: 0.9025 (pttp) REVERT: D 120 LYS cc_start: 0.9368 (tttp) cc_final: 0.9095 (ttpp) REVERT: E 79 LYS cc_start: 0.9324 (tptm) cc_final: 0.9038 (tptt) REVERT: E 120 MET cc_start: 0.8546 (mmm) cc_final: 0.8281 (mmm) REVERT: E 122 LYS cc_start: 0.9227 (ptmt) cc_final: 0.8577 (ptmm) REVERT: E 125 GLN cc_start: 0.9482 (mt0) cc_final: 0.9109 (mp10) REVERT: E 133 GLU cc_start: 0.8601 (mp0) cc_final: 0.8254 (mp0) REVERT: F 44 LYS cc_start: 0.9385 (tptm) cc_final: 0.9051 (tppp) REVERT: F 79 LYS cc_start: 0.9057 (mtpp) cc_final: 0.8702 (mtmm) REVERT: F 84 MET cc_start: 0.8615 (mmm) cc_final: 0.7381 (mmm) REVERT: F 88 TYR cc_start: 0.8672 (m-10) cc_final: 0.7318 (m-80) REVERT: F 95 ARG cc_start: 0.8813 (mtp85) cc_final: 0.8512 (mtt90) REVERT: G 25 PHE cc_start: 0.8890 (m-80) cc_final: 0.8638 (m-80) REVERT: G 32 ARG cc_start: 0.9383 (ttp80) cc_final: 0.8883 (tmm-80) REVERT: G 36 LYS cc_start: 0.9238 (mmtm) cc_final: 0.8802 (mmtm) REVERT: G 38 ASN cc_start: 0.9225 (m-40) cc_final: 0.8928 (m-40) REVERT: G 42 ARG cc_start: 0.8890 (ptp-110) cc_final: 0.7942 (ptm-80) REVERT: G 75 LYS cc_start: 0.9266 (mmtt) cc_final: 0.9004 (mmtm) REVERT: H 33 ARG cc_start: 0.8360 (mmm160) cc_final: 0.7787 (tpp80) REVERT: H 37 TYR cc_start: 0.9377 (m-80) cc_final: 0.9029 (m-80) REVERT: H 42 TYR cc_start: 0.8814 (t80) cc_final: 0.8530 (t80) REVERT: H 70 PHE cc_start: 0.9359 (t80) cc_final: 0.9110 (t80) REVERT: H 84 ASN cc_start: 0.9085 (m-40) cc_final: 0.8564 (m-40) REVERT: H 86 ARG cc_start: 0.9363 (tpp80) cc_final: 0.8935 (tpp80) REVERT: H 92 ARG cc_start: 0.8872 (mtp-110) cc_final: 0.8084 (ttp80) REVERT: N 38 MET cc_start: 0.4152 (ppp) cc_final: 0.3872 (ppp) REVERT: N 79 ASN cc_start: 0.6539 (p0) cc_final: 0.6109 (p0) REVERT: N 140 GLU cc_start: 0.9194 (pt0) cc_final: 0.8884 (pt0) REVERT: N 143 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8524 (mm-40) outliers start: 28 outliers final: 20 residues processed: 422 average time/residue: 0.1506 time to fit residues: 87.7253 Evaluate side-chains 429 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 407 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 55 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 88 THR 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 F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 97 LEU 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 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: 0.7980 chunk 116 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN 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 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 = 0.3204 r_free = 0.3204 target = 0.051818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.041347 restraints weight = 94171.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.042549 restraints weight = 43881.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.043394 restraints weight = 26424.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.043937 restraints weight = 18543.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.044073 restraints weight = 14821.004| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 15436 Z= 0.176 Angle : 0.872 19.535 22114 Z= 0.454 Chirality : 0.049 0.385 2519 Planarity : 0.005 0.069 1788 Dihedral : 30.147 174.510 4403 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 2.85 % Allowed : 36.36 % 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: 0.17 (0.25), residues: 1062 helix: 0.72 (0.19), residues: 661 sheet: 0.62 (1.20), residues: 24 loop : -0.91 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG M 112 TYR 0.016 0.001 TYR B 51 PHE 0.053 0.003 PHE A 67 TRP 0.004 0.001 TRP N 141 HIS 0.005 0.001 HIS K 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (15420) covalent geometry : angle 0.85073 / 0.45 (22096) hydrogen bonds : bond 0.04822 / 3.28 ( 872) hydrogen bonds : angle 3.96223 / 2.78 ( 2220) metal coordination : bond 0.02496 / 1.26 ( 16) metal coordination : angle 6.83756 / 3.53 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2665.75 seconds wall clock time: 46 minutes 49.55 seconds (2809.55 seconds total)