Starting phenix.real_space_refine on Sat Aug 23 23:08:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8grq_34212/08_2025/8grq_34212.cif Found real_map, /net/cci-nas-00/data/ceres_data/8grq_34212/08_2025/8grq_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_34212/08_2025/8grq_34212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8grq_34212/08_2025/8grq_34212.map" model { file = "/net/cci-nas-00/data/ceres_data/8grq_34212/08_2025/8grq_34212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8grq_34212/08_2025/8grq_34212.cif" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1168 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 294 5.49 5 S 36 5.16 5 C 8230 2.51 5 N 2706 2.21 5 O 3293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 3.16, 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: 1.09 Conformation dependent library (CDL) restraints added in 402.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.80 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: 2.10 Time building geometry restraints manager: 1.46 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=" CG GLU M 45 " pdb=" CD GLU M 45 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.66e+00 bond pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.64e+00 bond pdb=" CB ASP F 24 " pdb=" CG ASP F 24 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.53e+00 bond pdb=" CA ASP F 24 " pdb=" CB ASP F 24 " ideal model delta sigma weight residual 1.532 1.549 -0.017 1.43e-02 4.89e+03 1.43e+00 bond pdb=" CB CYS K 61 " pdb=" SG CYS K 61 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.37e+00 ... (remaining 15415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 21513 1.86 - 3.72: 520 3.72 - 5.59: 47 5.59 - 7.45: 13 7.45 - 9.31: 3 Bond angle restraints: 22096 Sorted by residual: angle pdb=" N SER A 96 " pdb=" CA SER A 96 " pdb=" C SER A 96 " ideal model delta sigma weight residual 110.97 115.40 -4.43 1.09e+00 8.42e-01 1.65e+01 angle pdb=" N GLU M 45 " pdb=" CA GLU M 45 " pdb=" CB GLU M 45 " ideal model delta sigma weight residual 110.28 116.43 -6.15 1.55e+00 4.16e-01 1.57e+01 angle pdb=" C LEU B 62 " pdb=" N GLU B 63 " pdb=" CA GLU B 63 " ideal model delta sigma weight residual 121.18 114.05 7.13 1.98e+00 2.55e-01 1.30e+01 angle pdb=" C LYS K 45 " pdb=" N PHE K 46 " pdb=" CA PHE K 46 " ideal model delta sigma weight residual 121.54 128.13 -6.59 1.91e+00 2.74e-01 1.19e+01 angle pdb=" CB LYS N 63 " pdb=" CG LYS N 63 " pdb=" CD LYS N 63 " ideal model delta sigma weight residual 111.30 119.12 -7.82 2.30e+00 1.89e-01 1.16e+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 - 0.034: 1788 0.034 - 0.068: 543 0.068 - 0.103: 137 0.103 - 0.137: 46 0.137 - 0.171: 5 Chirality restraints: 2519 Sorted by residual: 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 chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 2516 not shown) Planarity restraints: 1788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 109 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C LEU A 109 " 0.031 2.00e-02 2.50e+03 pdb=" O LEU A 109 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A 110 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS K 45 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C LYS K 45 " 0.031 2.00e-02 2.50e+03 pdb=" O LYS K 45 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE K 46 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE K 46 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C PHE K 46 " -0.029 2.00e-02 2.50e+03 pdb=" O PHE K 46 " 0.011 2.00e-02 2.50e+03 pdb=" N CYS K 47 " 0.010 2.00e-02 2.50e+03 ... (remaining 1785 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 512 2.68 - 3.24: 13853 3.24 - 3.79: 28007 3.79 - 4.35: 34420 4.35 - 4.90: 49151 Nonbonded interactions: 125943 Sorted by model distance: nonbonded pdb=" N2 DG I -10 " pdb=" O2 DC J 10 " model vdw 2.125 2.496 nonbonded pdb=" O GLN M 106 " pdb=" OG SER M 109 " model vdw 2.199 3.040 nonbonded pdb=" NH1 ARG F 92 " pdb=" OE2 GLU H 76 " model vdw 2.205 3.120 nonbonded pdb=" OH TYR C 57 " pdb=" NH1 ARG K 71 " model vdw 2.209 3.120 nonbonded pdb=" O ARG N 139 " pdb=" OG1 THR N 142 " model vdw 2.210 3.040 ... (remaining 125938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 10 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.200 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 15436 Z= 0.179 Angle : 0.693 14.367 22114 Z= 0.408 Chirality : 0.037 0.171 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 aren 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 covalent geometry : bond 0.00371 (15420) covalent geometry : angle 0.66945 (22096) hydrogen bonds : bond 0.14169 ( 872) hydrogen bonds : angle 5.32690 ( 2220) metal coordination : bond 0.03062 ( 16) metal coordination : angle 6.26842 ( 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 : 0.411 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: 0.9373 (m-80) cc_final: 0.9028 (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: 0.8665 (m-10) cc_final: 0.8348 (m-10) REVERT: H 86 ARG cc_start: 0.9190 (tpp80) cc_final: 0.8793 (tpp80) REVERT: H 101 LEU cc_start: 0.9258 (mp) cc_final: 0.8840 (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: 0.1507 time to fit residues: 107.3598 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 : 0.500 ------------------------------------------------------------------------------- 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: 8.9990 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: 7.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** K 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** K 54 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** N 143 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.048724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.038106 restraints weight = 96039.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.039329 restraints weight = 44882.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.040116 restraints weight = 26960.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.040684 restraints weight = 19062.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.040941 restraints weight = 15104.690| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 15436 Z= 0.373 Angle : 0.829 19.996 22114 Z= 0.448 Chirality : 0.046 0.216 2519 Planarity : 0.006 0.045 1788 Dihedral : 29.513 169.193 4404 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.67 % Favored : 96.23 % Rotamer: Outliers : 6.13 % Allowed : 19.61 % 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 aren not related in a simple way. whole: 0.44 (0.25), residues: 1062 helix: 0.96 (0.19), residues: 672 sheet: 0.67 (1.19), residues: 24 loop : -0.91 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 42 TYR 0.046 0.003 TYR D 83 PHE 0.034 0.002 PHE F 61 TRP 0.004 0.001 TRP N 33 HIS 0.009 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00835 (15420) covalent geometry : angle 0.78940 (22096) hydrogen bonds : bond 0.07475 ( 872) hydrogen bonds : angle 4.16119 ( 2220) metal coordination : bond 0.02923 ( 16) metal coordination : angle 8.90140 ( 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 499 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 443 time to evaluate : 0.434 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 80 THR cc_start: 0.9425 (OUTLIER) cc_final: 0.9200 (p) REVERT: A 94 GLU cc_start: 0.9344 (mm-30) cc_final: 0.8869 (mm-30) REVERT: A 109 LEU cc_start: 0.9461 (mp) cc_final: 0.9241 (mt) REVERT: A 129 ARG cc_start: 0.8842 (tpm170) cc_final: 0.8534 (tpm170) REVERT: B 49 LEU cc_start: 0.9051 (mm) cc_final: 0.8671 (mt) REVERT: B 52 GLU cc_start: 0.8452 (pm20) cc_final: 0.7949 (pm20) REVERT: C 54 VAL cc_start: 0.9694 (OUTLIER) cc_final: 0.9457 (p) REVERT: C 90 ASP cc_start: 0.9221 (t0) cc_final: 0.9015 (t0) REVERT: C 101 THR cc_start: 0.9165 (m) cc_final: 0.8662 (p) REVERT: C 104 GLN cc_start: 0.8611 (mp-120) cc_final: 0.8240 (mp10) REVERT: C 115 LEU cc_start: 0.9333 (mt) cc_final: 0.9097 (mt) REVERT: D 35 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6951 (mm-30) REVERT: D 68 ASP cc_start: 0.9406 (t0) cc_final: 0.9063 (t0) REVERT: D 88 THR cc_start: 0.9657 (m) cc_final: 0.9385 (p) REVERT: D 89 ILE cc_start: 0.9154 (mm) cc_final: 0.8933 (mm) REVERT: D 96 THR cc_start: 0.9598 (m) cc_final: 0.9369 (p) REVERT: D 105 GLU cc_start: 0.8332 (pm20) cc_final: 0.8063 (pm20) REVERT: E 50 GLU cc_start: 0.9418 (pt0) cc_final: 0.8924 (pt0) REVERT: E 90 MET cc_start: 0.8984 (mmp) cc_final: 0.8733 (mmm) REVERT: E 120 MET cc_start: 0.8501 (mmm) cc_final: 0.8123 (mmm) REVERT: E 122 LYS cc_start: 0.9249 (ptmt) cc_final: 0.8944 (ptmt) REVERT: E 125 GLN cc_start: 0.9501 (mt0) cc_final: 0.9175 (mp10) REVERT: E 133 GLU cc_start: 0.8101 (mp0) cc_final: 0.7820 (mp0) REVERT: F 35 ARG cc_start: 0.9471 (mtp-110) cc_final: 0.9251 (ttm-80) REVERT: F 39 ARG cc_start: 0.9340 (mmt90) cc_final: 0.8814 (mmt90) REVERT: F 49 LEU cc_start: 0.9297 (mt) cc_final: 0.8889 (mm) REVERT: F 78 ARG cc_start: 0.8812 (ttp-110) cc_final: 0.8591 (ttm110) REVERT: F 79 LYS cc_start: 0.9148 (mtpp) cc_final: 0.8823 (mtmm) REVERT: F 95 ARG cc_start: 0.8939 (mtp85) cc_final: 0.8608 (mtt90) REVERT: G 32 ARG cc_start: 0.9283 (ttp80) cc_final: 0.9049 (ttp80) REVERT: G 35 ARG cc_start: 0.8882 (mtm110) cc_final: 0.8570 (mtm-85) REVERT: G 61 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8946 (mm-30) REVERT: G 75 LYS cc_start: 0.9413 (mttm) cc_final: 0.9144 (mmmm) REVERT: H 37 TYR cc_start: 0.9486 (m-80) cc_final: 0.9200 (m-80) REVERT: H 40 TYR cc_start: 0.9457 (m-80) cc_final: 0.8871 (m-80) REVERT: H 47 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8796 (tm-30) REVERT: H 84 ASN cc_start: 0.9172 (m110) cc_final: 0.8811 (m110) REVERT: H 86 ARG cc_start: 0.9355 (tpp80) cc_final: 0.8982 (tpp80) REVERT: K 50 LYS cc_start: 0.9191 (mptt) cc_final: 0.8953 (mmtt) REVERT: K 71 ARG cc_start: 0.8552 (tmm-80) cc_final: 0.8351 (tmm-80) REVERT: K 79 PHE cc_start: 0.8949 (t80) cc_final: 0.8706 (t80) REVERT: M 104 MET cc_start: 0.9046 (mmm) cc_final: 0.8751 (mmm) REVERT: N 37 ILE cc_start: 0.7603 (pt) cc_final: 0.7350 (pt) REVERT: N 38 MET cc_start: 0.3340 (ppp) cc_final: 0.3036 (ppp) REVERT: N 79 ASN cc_start: 0.6546 (p0) cc_final: 0.6243 (p0) REVERT: N 135 ASN cc_start: 0.8238 (t0) cc_final: 0.7944 (t0) outliers start: 56 outliers final: 37 residues processed: 462 average time/residue: 0.1406 time to fit residues: 89.4425 Evaluate side-chains 441 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 402 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 B residue 43 VAL Chi-restraints excluded: chain B residue 50 ILE 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 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 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 112 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 43 VAL 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 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR 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 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: 10.0000 chunk 107 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 124 optimal weight: 30.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN G 31 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.050514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.039811 restraints weight = 95279.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.041032 restraints weight = 44670.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.041843 restraints weight = 26898.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.042408 restraints weight = 19024.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.042843 restraints weight = 15161.189| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 15436 Z= 0.206 Angle : 0.719 15.391 22114 Z= 0.390 Chirality : 0.040 0.274 2519 Planarity : 0.005 0.044 1788 Dihedral : 29.597 170.528 4403 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.95 % Rotamer: Outliers : 5.04 % Allowed : 24.97 % Favored : 69.99 % 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 aren not related in a simple way. whole: 0.60 (0.26), residues: 1062 helix: 1.14 (0.20), residues: 661 sheet: 0.82 (1.26), residues: 24 loop : -0.90 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 29 TYR 0.034 0.002 TYR D 83 PHE 0.024 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 covalent geometry : bond 0.00463 (15420) covalent geometry : angle 0.68611 (22096) hydrogen bonds : bond 0.04589 ( 872) hydrogen bonds : angle 3.71244 ( 2220) metal coordination : bond 0.02804 ( 16) metal coordination : angle 7.58099 ( 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 502 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 456 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9058 (tp40) cc_final: 0.8018 (tp40) REVERT: A 129 ARG cc_start: 0.8818 (tpm170) cc_final: 0.8422 (tpm170) REVERT: B 24 ASP cc_start: 0.7980 (t0) cc_final: 0.7620 (t0) REVERT: B 49 LEU cc_start: 0.8990 (mm) cc_final: 0.8608 (tp) REVERT: C 27 VAL cc_start: 0.9240 (m) cc_final: 0.9011 (p) REVERT: C 39 TYR cc_start: 0.9454 (m-80) cc_final: 0.9206 (m-80) REVERT: C 56 GLU cc_start: 0.9368 (mt-10) cc_final: 0.9167 (mt-10) REVERT: C 68 ASN cc_start: 0.9076 (m110) cc_final: 0.8836 (m110) REVERT: C 75 LYS cc_start: 0.8693 (mmmm) cc_final: 0.8406 (mmmm) REVERT: C 84 GLN cc_start: 0.9377 (tp40) cc_final: 0.9130 (tp40) REVERT: C 95 LYS cc_start: 0.9411 (tttp) cc_final: 0.9191 (tptp) REVERT: C 97 LEU cc_start: 0.9339 (mt) cc_final: 0.9112 (mp) REVERT: C 101 THR cc_start: 0.9019 (m) cc_final: 0.8499 (p) REVERT: D 35 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6916 (mm-30) REVERT: D 68 ASP cc_start: 0.9420 (t0) cc_final: 0.9100 (t0) REVERT: D 71 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8722 (tm-30) REVERT: D 88 THR cc_start: 0.9551 (m) cc_final: 0.9260 (p) REVERT: D 96 THR cc_start: 0.9613 (m) cc_final: 0.9290 (p) REVERT: E 50 GLU cc_start: 0.9376 (pt0) cc_final: 0.8579 (pt0) REVERT: E 120 MET cc_start: 0.8500 (mmm) cc_final: 0.8097 (mmm) REVERT: E 125 GLN cc_start: 0.9488 (mt0) cc_final: 0.9174 (mp10) REVERT: E 133 GLU cc_start: 0.8175 (mp0) cc_final: 0.7935 (mp0) REVERT: F 27 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8718 (mp10) REVERT: F 31 LYS cc_start: 0.9571 (tttm) cc_final: 0.9339 (tttp) REVERT: F 35 ARG cc_start: 0.9428 (mtp-110) cc_final: 0.9050 (ttm-80) REVERT: F 44 LYS cc_start: 0.9371 (tptm) cc_final: 0.8975 (mmmt) REVERT: F 49 LEU cc_start: 0.9268 (mt) cc_final: 0.9068 (mm) REVERT: F 59 LYS cc_start: 0.9590 (ptmm) cc_final: 0.9336 (ptmm) REVERT: F 79 LYS cc_start: 0.9084 (mtpp) cc_final: 0.8774 (mtmm) REVERT: F 92 ARG cc_start: 0.9343 (mtp-110) cc_final: 0.8931 (ttt-90) REVERT: F 93 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8418 (mp10) REVERT: F 95 ARG cc_start: 0.8850 (mtp85) cc_final: 0.8560 (mtt90) REVERT: G 32 ARG cc_start: 0.9346 (ttp80) cc_final: 0.8961 (ttp80) REVERT: G 38 ASN cc_start: 0.9244 (m-40) cc_final: 0.8861 (t0) REVERT: G 42 ARG cc_start: 0.8746 (ptp-110) cc_final: 0.8085 (ptm-80) REVERT: G 81 ARG cc_start: 0.9253 (tpt170) cc_final: 0.8971 (tpt170) REVERT: H 37 TYR cc_start: 0.9420 (m-80) cc_final: 0.9071 (m-80) REVERT: H 40 TYR cc_start: 0.9314 (m-80) cc_final: 0.8850 (m-80) REVERT: H 47 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8652 (tm-30) REVERT: H 72 ARG cc_start: 0.9441 (ttm170) cc_final: 0.9213 (ttm170) REVERT: H 83 TYR cc_start: 0.8862 (m-10) cc_final: 0.8446 (m-80) REVERT: H 84 ASN cc_start: 0.9095 (m110) cc_final: 0.8590 (m110) REVERT: H 86 ARG cc_start: 0.9389 (tpp80) cc_final: 0.8898 (tpp80) REVERT: K 50 LYS cc_start: 0.9199 (mptt) cc_final: 0.8967 (mmtp) REVERT: K 66 ASN cc_start: 0.9306 (t0) cc_final: 0.9032 (t0) REVERT: N 37 ILE cc_start: 0.7632 (pt) cc_final: 0.7373 (pt) REVERT: N 38 MET cc_start: 0.3467 (ppp) cc_final: 0.3111 (ppp) REVERT: N 79 ASN cc_start: 0.6563 (p0) cc_final: 0.6185 (p0) outliers start: 46 outliers final: 28 residues processed: 469 average time/residue: 0.1583 time to fit residues: 101.8581 Evaluate side-chains 434 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 404 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 107 THR 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 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 F residue 37 LEU Chi-restraints excluded: chain F residue 63 GLU 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 87 VAL Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain K residue 51 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 29 optimal weight: 3.9990 chunk 110 optimal weight: 40.0000 chunk 56 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 99 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.049561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.038993 restraints weight = 95481.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.040186 restraints weight = 44273.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.041007 restraints weight = 26811.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.041557 restraints weight = 18874.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.041968 restraints weight = 15007.785| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 15436 Z= 0.259 Angle : 0.759 16.083 22114 Z= 0.406 Chirality : 0.042 0.248 2519 Planarity : 0.005 0.068 1788 Dihedral : 29.736 170.236 4403 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.91 % Allowed : 27.16 % Favored : 66.92 % 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 aren not related in a simple way. whole: 0.56 (0.26), residues: 1062 helix: 1.07 (0.20), residues: 673 sheet: 0.72 (1.26), residues: 24 loop : -0.92 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 92 TYR 0.024 0.002 TYR D 83 PHE 0.031 0.002 PHE F 61 TRP 0.004 0.001 TRP N 141 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00586 (15420) covalent geometry : angle 0.72310 (22096) hydrogen bonds : bond 0.05374 ( 872) hydrogen bonds : angle 3.80837 ( 2220) metal coordination : bond 0.02908 ( 16) metal coordination : angle 8.16105 ( 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 489 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 435 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9598 (t80) cc_final: 0.9386 (t80) REVERT: A 93 GLN cc_start: 0.8744 (tp40) cc_final: 0.8518 (tp40) REVERT: A 94 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8638 (mm-30) REVERT: A 112 ILE cc_start: 0.9495 (pt) cc_final: 0.9166 (mt) REVERT: A 129 ARG cc_start: 0.8888 (tpm170) cc_final: 0.8444 (tpm170) REVERT: B 24 ASP cc_start: 0.8279 (t0) cc_final: 0.8009 (t0) REVERT: C 27 VAL cc_start: 0.9307 (OUTLIER) cc_final: 0.9036 (p) REVERT: C 39 TYR cc_start: 0.9465 (m-80) cc_final: 0.9172 (m-80) REVERT: C 56 GLU cc_start: 0.9373 (mt-10) cc_final: 0.8978 (mt-10) REVERT: C 68 ASN cc_start: 0.9162 (m110) cc_final: 0.8910 (m110) REVERT: C 74 LYS cc_start: 0.9426 (mmmm) cc_final: 0.9211 (mmmt) REVERT: C 84 GLN cc_start: 0.9388 (tp40) cc_final: 0.9090 (tp40) REVERT: C 95 LYS cc_start: 0.9424 (tttp) cc_final: 0.9204 (tptp) REVERT: C 101 THR cc_start: 0.8962 (m) cc_final: 0.8417 (p) REVERT: D 68 ASP cc_start: 0.9456 (t0) cc_final: 0.9235 (t0) REVERT: D 71 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8750 (tm-30) REVERT: D 80 LEU cc_start: 0.9665 (OUTLIER) cc_final: 0.9423 (tp) REVERT: D 93 GLU cc_start: 0.9079 (pm20) cc_final: 0.8834 (pm20) REVERT: D 96 THR cc_start: 0.9602 (m) cc_final: 0.9301 (p) REVERT: E 120 MET cc_start: 0.8553 (mmm) cc_final: 0.8102 (mmm) REVERT: E 122 LYS cc_start: 0.9244 (ptmt) cc_final: 0.8817 (ptmt) REVERT: E 125 GLN cc_start: 0.9505 (mt0) cc_final: 0.9173 (mp10) REVERT: E 133 GLU cc_start: 0.8165 (mp0) cc_final: 0.7929 (mp0) REVERT: F 27 GLN cc_start: 0.9269 (mm-40) cc_final: 0.8724 (mp10) REVERT: F 30 THR cc_start: 0.9258 (p) cc_final: 0.9028 (t) REVERT: F 35 ARG cc_start: 0.9371 (mtp-110) cc_final: 0.9115 (ttm-80) REVERT: F 44 LYS cc_start: 0.9400 (tptm) cc_final: 0.8814 (mmmt) REVERT: F 95 ARG cc_start: 0.8851 (mtp85) cc_final: 0.8569 (mtt90) REVERT: G 32 ARG cc_start: 0.9365 (ttp80) cc_final: 0.8983 (tmm-80) REVERT: G 38 ASN cc_start: 0.9319 (m-40) cc_final: 0.8843 (t0) REVERT: G 42 ARG cc_start: 0.8799 (ptp-110) cc_final: 0.8092 (ptm-80) REVERT: G 61 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8819 (mm-30) REVERT: G 81 ARG cc_start: 0.9232 (tpt170) cc_final: 0.8805 (tpt170) REVERT: H 37 TYR cc_start: 0.9547 (m-80) cc_final: 0.9226 (m-80) REVERT: H 40 TYR cc_start: 0.9405 (m-80) cc_final: 0.8752 (m-80) REVERT: H 47 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8738 (tm-30) REVERT: H 83 TYR cc_start: 0.8807 (m-10) cc_final: 0.8564 (m-80) REVERT: H 84 ASN cc_start: 0.9034 (m110) cc_final: 0.8500 (m-40) REVERT: H 86 ARG cc_start: 0.9378 (tpp80) cc_final: 0.8850 (tpp80) REVERT: K 50 LYS cc_start: 0.9202 (mptt) cc_final: 0.8928 (mmtp) REVERT: K 66 ASN cc_start: 0.9386 (t0) cc_final: 0.9132 (t0) REVERT: M 104 MET cc_start: 0.8984 (mmm) cc_final: 0.8726 (mmm) REVERT: N 37 ILE cc_start: 0.7580 (pt) cc_final: 0.7233 (pt) REVERT: N 38 MET cc_start: 0.3285 (ppp) cc_final: 0.2914 (ppp) REVERT: N 79 ASN cc_start: 0.6565 (p0) cc_final: 0.6172 (p0) outliers start: 54 outliers final: 38 residues processed: 454 average time/residue: 0.1579 time to fit residues: 98.2562 Evaluate side-chains 452 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 411 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 50 ILE 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 38 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 80 LEU 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 109 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 63 GLU 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 G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain M residue 61 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 38 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS K 53 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.050229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.039551 restraints weight = 95163.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.040773 restraints weight = 43543.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.041599 restraints weight = 26207.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.042136 restraints weight = 18418.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.042571 restraints weight = 14750.658| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 15436 Z= 0.210 Angle : 0.736 15.005 22114 Z= 0.392 Chirality : 0.041 0.302 2519 Planarity : 0.005 0.043 1788 Dihedral : 29.799 170.839 4403 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 6.02 % Allowed : 28.48 % Favored : 65.50 % 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 aren not related in a simple way. whole: 0.53 (0.26), residues: 1062 helix: 1.04 (0.19), residues: 674 sheet: 0.71 (1.26), residues: 24 loop : -0.89 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 92 TYR 0.018 0.002 TYR D 83 PHE 0.026 0.002 PHE F 61 TRP 0.004 0.001 TRP N 141 HIS 0.004 0.001 HIS K 41 Details of bonding type rmsd covalent geometry : bond 0.00476 (15420) covalent geometry : angle 0.70293 (22096) hydrogen bonds : bond 0.04600 ( 872) hydrogen bonds : angle 3.66853 ( 2220) metal coordination : bond 0.02745 ( 16) metal coordination : angle 7.64599 ( 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 495 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 440 time to evaluate : 0.466 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 67 PHE cc_start: 0.9584 (t80) cc_final: 0.9263 (t80) REVERT: A 93 GLN cc_start: 0.9014 (tp40) cc_final: 0.8755 (tp40) REVERT: A 94 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8516 (mt-10) REVERT: A 112 ILE cc_start: 0.9475 (pt) cc_final: 0.9171 (mt) REVERT: A 129 ARG cc_start: 0.8932 (tpm170) cc_final: 0.8470 (tpm170) REVERT: B 24 ASP cc_start: 0.8399 (t0) cc_final: 0.8127 (t0) REVERT: B 63 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8480 (pm20) REVERT: C 27 VAL cc_start: 0.9289 (OUTLIER) cc_final: 0.9007 (p) REVERT: C 39 TYR cc_start: 0.9434 (m-80) cc_final: 0.9200 (m-80) REVERT: C 56 GLU cc_start: 0.9372 (mt-10) cc_final: 0.9152 (mt-10) REVERT: C 68 ASN cc_start: 0.9163 (m110) cc_final: 0.8955 (m110) REVERT: C 74 LYS cc_start: 0.9374 (mmmm) cc_final: 0.9128 (mmmt) REVERT: C 75 LYS cc_start: 0.8588 (mmmm) cc_final: 0.8148 (mmmm) REVERT: C 84 GLN cc_start: 0.9377 (tp40) cc_final: 0.9071 (tp40) REVERT: C 95 LYS cc_start: 0.9370 (tttp) cc_final: 0.9166 (tptp) REVERT: C 101 THR cc_start: 0.8869 (m) cc_final: 0.8348 (p) REVERT: D 47 GLN cc_start: 0.9333 (tm-30) cc_final: 0.9002 (tm-30) REVERT: D 59 MET cc_start: 0.9606 (tpt) cc_final: 0.9405 (tpt) REVERT: D 68 ASP cc_start: 0.9483 (t0) cc_final: 0.9248 (t0) REVERT: D 71 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8724 (tm-30) REVERT: D 93 GLU cc_start: 0.9110 (pm20) cc_final: 0.8727 (pm20) REVERT: D 96 THR cc_start: 0.9579 (m) cc_final: 0.9276 (p) REVERT: D 105 GLU cc_start: 0.8359 (pm20) cc_final: 0.7945 (pm20) REVERT: D 108 LYS cc_start: 0.9495 (ptpp) cc_final: 0.9190 (pttp) REVERT: E 105 GLU cc_start: 0.8717 (pp20) cc_final: 0.8165 (pp20) REVERT: E 120 MET cc_start: 0.8564 (mmm) cc_final: 0.8096 (mmm) REVERT: E 122 LYS cc_start: 0.9248 (ptmt) cc_final: 0.8819 (ptmt) REVERT: E 125 GLN cc_start: 0.9505 (mt0) cc_final: 0.9171 (mp10) REVERT: E 133 GLU cc_start: 0.8166 (mp0) cc_final: 0.7880 (mp0) REVERT: F 35 ARG cc_start: 0.9358 (mtp-110) cc_final: 0.9096 (ttm-80) REVERT: F 44 LYS cc_start: 0.9400 (tptm) cc_final: 0.8934 (mmmt) REVERT: F 79 LYS cc_start: 0.9098 (mtpp) cc_final: 0.8849 (mtmm) REVERT: F 95 ARG cc_start: 0.8836 (mtp85) cc_final: 0.8554 (mtt90) REVERT: G 32 ARG cc_start: 0.9362 (ttp80) cc_final: 0.8617 (ttp80) REVERT: G 36 LYS cc_start: 0.9381 (mmmm) cc_final: 0.8967 (mmtm) REVERT: G 38 ASN cc_start: 0.9301 (m-40) cc_final: 0.8935 (t0) REVERT: G 42 ARG cc_start: 0.8773 (ptp-110) cc_final: 0.8067 (ptm-80) REVERT: G 81 ARG cc_start: 0.9165 (tpt170) cc_final: 0.8729 (tpt170) REVERT: G 90 ASP cc_start: 0.8546 (t0) cc_final: 0.8266 (t0) REVERT: H 37 TYR cc_start: 0.9543 (m-80) cc_final: 0.9156 (m-80) REVERT: H 47 GLN cc_start: 0.9038 (tm-30) cc_final: 0.8721 (tm-30) REVERT: H 70 PHE cc_start: 0.9378 (t80) cc_final: 0.9125 (t80) REVERT: H 83 TYR cc_start: 0.8774 (m-10) cc_final: 0.8524 (m-10) REVERT: H 84 ASN cc_start: 0.8999 (m110) cc_final: 0.8590 (m-40) REVERT: H 86 ARG cc_start: 0.9373 (tpp80) cc_final: 0.9013 (tpp80) REVERT: H 96 THR cc_start: 0.9637 (m) cc_final: 0.9383 (p) REVERT: K 43 PHE cc_start: 0.7898 (m-10) cc_final: 0.7517 (m-80) REVERT: M 104 MET cc_start: 0.9070 (mmm) cc_final: 0.8758 (mmm) REVERT: N 29 ASP cc_start: 0.6803 (t70) cc_final: 0.6158 (p0) REVERT: N 37 ILE cc_start: 0.7685 (pt) cc_final: 0.7422 (pt) REVERT: N 38 MET cc_start: 0.3429 (ppp) cc_final: 0.2960 (ppp) REVERT: N 79 ASN cc_start: 0.6553 (p0) cc_final: 0.6139 (p0) REVERT: N 140 GLU cc_start: 0.9211 (pt0) cc_final: 0.9006 (pt0) outliers start: 55 outliers final: 37 residues processed: 457 average time/residue: 0.1525 time to fit residues: 95.7793 Evaluate side-chains 442 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 402 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 ILE 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 27 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 32 SER 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 E residue 100 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 63 GLU 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 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 68 ASP 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 41 HIS Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 65 LYS 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: 8.9990 chunk 73 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 ASN ** 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 = 0.3153 r_free = 0.3153 target = 0.049743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.039018 restraints weight = 96051.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.040239 restraints weight = 44296.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.041037 restraints weight = 26691.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.041568 restraints weight = 19037.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.041988 restraints weight = 15285.440| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 15436 Z= 0.239 Angle : 0.763 16.066 22114 Z= 0.405 Chirality : 0.042 0.288 2519 Planarity : 0.005 0.045 1788 Dihedral : 29.880 170.655 4403 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.61 % Favored : 95.29 % Rotamer: Outliers : 5.81 % Allowed : 30.01 % Favored : 64.18 % 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 aren not related in a simple way. whole: 0.52 (0.26), residues: 1062 helix: 1.01 (0.19), residues: 672 sheet: 0.78 (1.26), residues: 24 loop : -0.85 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 71 TYR 0.017 0.002 TYR D 83 PHE 0.033 0.002 PHE E 67 TRP 0.004 0.001 TRP N 93 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00542 (15420) covalent geometry : angle 0.72979 (22096) hydrogen bonds : bond 0.05117 ( 872) hydrogen bonds : angle 3.75675 ( 2220) metal coordination : bond 0.02675 ( 16) metal coordination : angle 7.82190 ( 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 476 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 423 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.8906 (mt0) cc_final: 0.8574 (mp10) REVERT: A 93 GLN cc_start: 0.8688 (tp40) cc_final: 0.8404 (tp40) REVERT: A 94 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8752 (mm-30) REVERT: A 112 ILE cc_start: 0.9496 (pt) cc_final: 0.9183 (mt) REVERT: A 129 ARG cc_start: 0.8955 (tpm170) cc_final: 0.8490 (tpm170) REVERT: B 24 ASP cc_start: 0.8528 (t0) cc_final: 0.8212 (t0) REVERT: B 63 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8522 (pm20) REVERT: B 79 LYS cc_start: 0.9152 (mtmt) cc_final: 0.8653 (ptpt) REVERT: B 88 TYR cc_start: 0.9144 (m-10) cc_final: 0.8879 (m-10) REVERT: C 27 VAL cc_start: 0.9321 (OUTLIER) cc_final: 0.9038 (p) REVERT: C 39 TYR cc_start: 0.9460 (m-80) cc_final: 0.9238 (m-80) REVERT: C 56 GLU cc_start: 0.9364 (mt-10) cc_final: 0.9133 (mt-10) REVERT: C 64 GLU cc_start: 0.9335 (tm-30) cc_final: 0.9089 (tm-30) REVERT: C 68 ASN cc_start: 0.9306 (m110) cc_final: 0.8985 (m-40) REVERT: C 74 LYS cc_start: 0.9364 (mmmm) cc_final: 0.9128 (mmmt) REVERT: C 75 LYS cc_start: 0.8656 (mmmm) cc_final: 0.8316 (mmmm) REVERT: C 84 GLN cc_start: 0.9410 (tp40) cc_final: 0.9089 (tp-100) REVERT: C 95 LYS cc_start: 0.9382 (tttp) cc_final: 0.9159 (tptp) REVERT: C 101 THR cc_start: 0.8850 (m) cc_final: 0.8324 (p) REVERT: D 33 ARG cc_start: 0.8708 (tpt170) cc_final: 0.8382 (tpt170) REVERT: D 47 GLN cc_start: 0.9373 (tm-30) cc_final: 0.8986 (tm-30) REVERT: D 68 ASP cc_start: 0.9482 (t0) cc_final: 0.9265 (t0) REVERT: D 71 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8733 (tm-30) REVERT: D 96 THR cc_start: 0.9599 (m) cc_final: 0.9317 (p) REVERT: D 105 GLU cc_start: 0.8330 (pm20) cc_final: 0.7935 (pm20) REVERT: D 108 LYS cc_start: 0.9492 (ptpp) cc_final: 0.9184 (pttp) REVERT: E 50 GLU cc_start: 0.9465 (pt0) cc_final: 0.9200 (pt0) REVERT: E 79 LYS cc_start: 0.9416 (tptp) cc_final: 0.9084 (tptp) REVERT: E 105 GLU cc_start: 0.8735 (pp20) cc_final: 0.8318 (pp20) REVERT: E 120 MET cc_start: 0.8615 (mmm) cc_final: 0.8152 (mmm) REVERT: E 122 LYS cc_start: 0.9274 (ptmt) cc_final: 0.8825 (ptmt) REVERT: E 125 GLN cc_start: 0.9509 (mt0) cc_final: 0.9170 (mp10) REVERT: E 133 GLU cc_start: 0.8157 (mp0) cc_final: 0.7885 (mp0) REVERT: F 44 LYS cc_start: 0.9408 (tptm) cc_final: 0.8967 (mmmt) REVERT: F 78 ARG cc_start: 0.8625 (ttp80) cc_final: 0.8213 (ttp80) REVERT: F 79 LYS cc_start: 0.9099 (mtpp) cc_final: 0.8806 (mtmm) REVERT: F 95 ARG cc_start: 0.8839 (mtp85) cc_final: 0.8519 (mtt90) REVERT: G 32 ARG cc_start: 0.9401 (ttp80) cc_final: 0.8726 (ttp80) REVERT: G 36 LYS cc_start: 0.9388 (mmmm) cc_final: 0.8981 (mmtm) REVERT: G 38 ASN cc_start: 0.9326 (m-40) cc_final: 0.8872 (t0) REVERT: G 42 ARG cc_start: 0.8783 (ptp-110) cc_final: 0.8070 (ptm-80) REVERT: G 81 ARG cc_start: 0.9211 (tpt170) cc_final: 0.8712 (tpt170) REVERT: H 35 GLU cc_start: 0.7968 (tp30) cc_final: 0.7704 (tp30) REVERT: H 37 TYR cc_start: 0.9535 (m-80) cc_final: 0.9161 (m-80) REVERT: H 47 GLN cc_start: 0.9098 (tm-30) cc_final: 0.8792 (tm-30) REVERT: H 83 TYR cc_start: 0.8801 (m-10) cc_final: 0.8581 (m-10) REVERT: H 84 ASN cc_start: 0.9005 (m110) cc_final: 0.8588 (m-40) REVERT: H 86 ARG cc_start: 0.9367 (tpp80) cc_final: 0.8986 (tpp80) REVERT: M 104 MET cc_start: 0.9092 (mmm) cc_final: 0.8792 (mmm) REVERT: N 37 ILE cc_start: 0.7623 (pt) cc_final: 0.7360 (pt) REVERT: N 38 MET cc_start: 0.3242 (ppp) cc_final: 0.2821 (ppp) REVERT: N 79 ASN cc_start: 0.6567 (p0) cc_final: 0.6157 (p0) REVERT: N 140 GLU cc_start: 0.9201 (pt0) cc_final: 0.8958 (pt0) outliers start: 53 outliers final: 37 residues processed: 442 average time/residue: 0.1518 time to fit residues: 91.1482 Evaluate side-chains 446 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 406 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 ILE 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 27 VAL Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 32 SER 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 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 F residue 37 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 63 GLU 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 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 63 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 68 ASP 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 41 HIS Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain N residue 103 LEU 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: 0.7980 chunk 104 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 75 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.050582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.039950 restraints weight = 94749.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.041151 restraints weight = 44760.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.041937 restraints weight = 27264.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.042508 restraints weight = 19327.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.042913 restraints weight = 15377.652| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 15436 Z= 0.203 Angle : 0.759 14.383 22114 Z= 0.402 Chirality : 0.041 0.338 2519 Planarity : 0.005 0.045 1788 Dihedral : 29.858 170.913 4403 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 4.82 % Allowed : 31.87 % Favored : 63.31 % 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 aren not related in a simple way. whole: 0.53 (0.26), residues: 1062 helix: 1.04 (0.20), residues: 671 sheet: 0.67 (1.24), residues: 24 loop : -0.88 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 39 TYR 0.013 0.002 TYR D 83 PHE 0.040 0.002 PHE E 67 TRP 0.004 0.001 TRP N 93 HIS 0.004 0.001 HIS K 41 Details of bonding type rmsd covalent geometry : bond 0.00461 (15420) covalent geometry : angle 0.72870 (22096) hydrogen bonds : bond 0.04570 ( 872) hydrogen bonds : angle 3.71906 ( 2220) metal coordination : bond 0.02539 ( 16) metal coordination : angle 7.44804 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 428 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.8588 (m-80) cc_final: 0.8207 (m-80) REVERT: A 85 GLN cc_start: 0.8827 (mt0) cc_final: 0.8506 (mp10) REVERT: A 94 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8508 (mt-10) REVERT: A 129 ARG cc_start: 0.8922 (tpm170) cc_final: 0.8475 (tpm170) REVERT: B 24 ASP cc_start: 0.8437 (t0) cc_final: 0.8140 (t0) REVERT: B 59 LYS cc_start: 0.9322 (tppp) cc_final: 0.8905 (tppp) REVERT: B 63 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8487 (pm20) REVERT: B 88 TYR cc_start: 0.9144 (m-10) cc_final: 0.8930 (m-80) REVERT: C 27 VAL cc_start: 0.9324 (OUTLIER) cc_final: 0.9030 (p) REVERT: C 56 GLU cc_start: 0.9355 (mt-10) cc_final: 0.9124 (mt-10) REVERT: C 64 GLU cc_start: 0.9309 (tm-30) cc_final: 0.9050 (tm-30) REVERT: C 68 ASN cc_start: 0.9283 (m110) cc_final: 0.8924 (m-40) REVERT: C 74 LYS cc_start: 0.9336 (mmmm) cc_final: 0.9099 (mmmt) REVERT: C 75 LYS cc_start: 0.8744 (mmmm) cc_final: 0.8453 (mmmm) REVERT: C 95 LYS cc_start: 0.9366 (tttp) cc_final: 0.9148 (tptp) REVERT: C 101 THR cc_start: 0.8792 (m) cc_final: 0.8275 (p) REVERT: D 33 ARG cc_start: 0.8771 (tpt170) cc_final: 0.7949 (mmt90) REVERT: D 47 GLN cc_start: 0.9366 (tm-30) cc_final: 0.8982 (tm-30) REVERT: D 71 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8729 (tm-30) REVERT: D 80 LEU cc_start: 0.9658 (tp) cc_final: 0.9325 (tp) REVERT: D 96 THR cc_start: 0.9593 (m) cc_final: 0.9302 (p) REVERT: D 105 GLU cc_start: 0.8231 (pm20) cc_final: 0.7637 (pm20) REVERT: D 108 LYS cc_start: 0.9484 (ptpp) cc_final: 0.9139 (pttp) REVERT: E 105 GLU cc_start: 0.8770 (pp20) cc_final: 0.8333 (pp20) REVERT: E 120 MET cc_start: 0.8610 (mmm) cc_final: 0.8139 (mmm) REVERT: E 122 LYS cc_start: 0.9263 (ptmt) cc_final: 0.8813 (ptmt) REVERT: E 125 GLN cc_start: 0.9513 (mt0) cc_final: 0.9178 (mp10) REVERT: F 35 ARG cc_start: 0.9422 (ttm-80) cc_final: 0.8988 (ttm-80) REVERT: F 44 LYS cc_start: 0.9397 (tptm) cc_final: 0.9107 (mmmt) REVERT: F 78 ARG cc_start: 0.8596 (ttp80) cc_final: 0.8178 (ttp80) REVERT: F 79 LYS cc_start: 0.9073 (mtpp) cc_final: 0.8817 (mtmm) REVERT: F 93 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8616 (mp10) REVERT: F 95 ARG cc_start: 0.8846 (mtp85) cc_final: 0.8519 (mtt90) REVERT: G 32 ARG cc_start: 0.9349 (ttp80) cc_final: 0.8802 (tmm-80) REVERT: G 35 ARG cc_start: 0.8925 (mtm110) cc_final: 0.8218 (mtm-85) REVERT: G 36 LYS cc_start: 0.9307 (mmmm) cc_final: 0.9020 (mmtm) REVERT: G 38 ASN cc_start: 0.9266 (m-40) cc_final: 0.8950 (t0) REVERT: G 39 TYR cc_start: 0.9321 (m-80) cc_final: 0.8980 (m-80) REVERT: G 42 ARG cc_start: 0.8792 (ptp-110) cc_final: 0.8097 (ptm-80) REVERT: G 57 TYR cc_start: 0.9312 (t80) cc_final: 0.8874 (t80) REVERT: G 61 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8749 (mt-10) REVERT: G 75 LYS cc_start: 0.9331 (mmtt) cc_final: 0.8581 (mmmm) REVERT: G 81 ARG cc_start: 0.9222 (tpt170) cc_final: 0.8792 (tpt170) REVERT: H 33 ARG cc_start: 0.8536 (tpp80) cc_final: 0.8312 (tpp80) REVERT: H 35 GLU cc_start: 0.7990 (tp30) cc_final: 0.7754 (tp30) REVERT: H 37 TYR cc_start: 0.9482 (m-80) cc_final: 0.9167 (m-80) REVERT: H 40 TYR cc_start: 0.9420 (m-80) cc_final: 0.8949 (m-80) REVERT: H 47 GLN cc_start: 0.9082 (tm-30) cc_final: 0.8784 (tm-30) REVERT: H 84 ASN cc_start: 0.8924 (m110) cc_final: 0.8532 (m-40) REVERT: H 86 ARG cc_start: 0.9352 (tpp80) cc_final: 0.8965 (tpp80) REVERT: N 37 ILE cc_start: 0.7627 (pt) cc_final: 0.7356 (pt) REVERT: N 38 MET cc_start: 0.3247 (ppp) cc_final: 0.2818 (ppp) REVERT: N 79 ASN cc_start: 0.6504 (p0) cc_final: 0.6076 (p0) REVERT: N 140 GLU cc_start: 0.9211 (pt0) cc_final: 0.8996 (pt0) outliers start: 44 outliers final: 29 residues processed: 440 average time/residue: 0.1503 time to fit residues: 90.2728 Evaluate side-chains 438 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 405 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 50 ILE 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 27 VAL 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 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 E residue 100 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 63 GLU 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 93 GLN 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 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 N residue 103 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 111 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 118 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 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** N 7 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.051776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.041234 restraints weight = 94123.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.042410 restraints weight = 44376.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.043199 restraints weight = 27344.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.043759 restraints weight = 19460.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.043937 restraints weight = 15580.130| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 15436 Z= 0.172 Angle : 0.784 15.440 22114 Z= 0.410 Chirality : 0.041 0.339 2519 Planarity : 0.005 0.043 1788 Dihedral : 29.750 171.385 4403 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 4.49 % Allowed : 34.17 % Favored : 61.34 % 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 aren not related in a simple way. whole: 0.50 (0.26), residues: 1062 helix: 0.99 (0.20), residues: 672 sheet: 0.73 (1.27), residues: 24 loop : -0.84 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 112 TYR 0.028 0.002 TYR C 39 PHE 0.043 0.002 PHE E 67 TRP 0.003 0.001 TRP N 141 HIS 0.004 0.001 HIS K 41 Details of bonding type rmsd covalent geometry : bond 0.00388 (15420) covalent geometry : angle 0.75718 (22096) hydrogen bonds : bond 0.04307 ( 872) hydrogen bonds : angle 3.67266 ( 2220) metal coordination : bond 0.02500 ( 16) metal coordination : angle 7.23079 ( 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 476 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 435 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.8537 (m-80) cc_final: 0.8187 (m-80) REVERT: A 67 PHE cc_start: 0.9390 (t80) cc_final: 0.9040 (t80) REVERT: A 85 GLN cc_start: 0.8699 (mt0) cc_final: 0.8423 (mp10) REVERT: A 94 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8735 (mm-30) REVERT: A 97 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8273 (tp30) REVERT: A 129 ARG cc_start: 0.8935 (tpm170) cc_final: 0.8491 (tpm170) REVERT: B 24 ASP cc_start: 0.8391 (t0) cc_final: 0.8100 (t0) REVERT: B 63 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8486 (pm20) REVERT: B 88 TYR cc_start: 0.9124 (m-10) cc_final: 0.8902 (m-80) REVERT: C 27 VAL cc_start: 0.9214 (m) cc_final: 0.8834 (p) REVERT: C 41 GLU cc_start: 0.8690 (pm20) cc_final: 0.7948 (pp20) REVERT: C 56 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8963 (mt-10) REVERT: C 64 GLU cc_start: 0.9289 (tm-30) cc_final: 0.9023 (tm-30) REVERT: C 68 ASN cc_start: 0.9269 (m110) cc_final: 0.8899 (m-40) REVERT: C 74 LYS cc_start: 0.9311 (mmmm) cc_final: 0.9076 (mmmt) REVERT: C 75 LYS cc_start: 0.8724 (mmmm) cc_final: 0.8358 (mmmm) REVERT: C 84 GLN cc_start: 0.9450 (tp-100) cc_final: 0.8857 (tm-30) REVERT: C 95 LYS cc_start: 0.9343 (tttp) cc_final: 0.9135 (tptp) REVERT: C 101 THR cc_start: 0.8784 (m) cc_final: 0.8305 (p) REVERT: D 47 GLN cc_start: 0.9332 (tm-30) cc_final: 0.9012 (tm-30) REVERT: D 68 ASP cc_start: 0.9434 (t0) cc_final: 0.9082 (t0) REVERT: D 80 LEU cc_start: 0.9660 (tp) cc_final: 0.9387 (tp) REVERT: D 93 GLU cc_start: 0.9120 (pm20) cc_final: 0.8489 (pm20) REVERT: D 96 THR cc_start: 0.9573 (m) cc_final: 0.9290 (p) REVERT: E 79 LYS cc_start: 0.9307 (tptp) cc_final: 0.8910 (tptp) REVERT: E 105 GLU cc_start: 0.8745 (pp20) cc_final: 0.8305 (pp20) REVERT: E 120 MET cc_start: 0.8485 (mmm) cc_final: 0.8005 (mmm) REVERT: E 122 LYS cc_start: 0.9297 (ptmt) cc_final: 0.8982 (ptmt) REVERT: E 125 GLN cc_start: 0.9474 (mt0) cc_final: 0.9156 (mp10) REVERT: F 35 ARG cc_start: 0.9355 (ttm-80) cc_final: 0.8989 (ttm-80) REVERT: F 44 LYS cc_start: 0.9399 (tptm) cc_final: 0.8987 (mmmt) REVERT: F 78 ARG cc_start: 0.8534 (ttp80) cc_final: 0.8135 (ttp80) REVERT: F 79 LYS cc_start: 0.8986 (mtpp) cc_final: 0.8615 (mtmm) REVERT: F 85 ASP cc_start: 0.9246 (OUTLIER) cc_final: 0.9020 (p0) REVERT: F 92 ARG cc_start: 0.9450 (mmm-85) cc_final: 0.8980 (ttt-90) REVERT: F 93 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8601 (mp10) REVERT: G 32 ARG cc_start: 0.9354 (ttp80) cc_final: 0.8618 (ttp80) REVERT: G 35 ARG cc_start: 0.8886 (mtm110) cc_final: 0.8143 (mtm-85) REVERT: G 36 LYS cc_start: 0.9284 (mmmm) cc_final: 0.9014 (mmtm) REVERT: G 38 ASN cc_start: 0.9172 (m-40) cc_final: 0.8852 (t0) REVERT: G 42 ARG cc_start: 0.8780 (ptp-110) cc_final: 0.8094 (ptm-80) REVERT: G 57 TYR cc_start: 0.9205 (t80) cc_final: 0.8562 (t80) REVERT: G 61 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8671 (mt-10) REVERT: G 75 LYS cc_start: 0.9203 (mmtt) cc_final: 0.8879 (mmtm) REVERT: G 81 ARG cc_start: 0.9201 (tpt170) cc_final: 0.8598 (tpt170) REVERT: G 90 ASP cc_start: 0.8480 (t0) cc_final: 0.8260 (t0) REVERT: H 33 ARG cc_start: 0.8574 (tpp80) cc_final: 0.8280 (tpt170) REVERT: H 37 TYR cc_start: 0.9414 (m-80) cc_final: 0.9097 (m-80) REVERT: H 40 TYR cc_start: 0.9284 (m-80) cc_final: 0.8980 (m-80) REVERT: H 47 GLN cc_start: 0.9073 (tm-30) cc_final: 0.8772 (tm-30) REVERT: H 70 PHE cc_start: 0.9383 (t80) cc_final: 0.9116 (t80) REVERT: H 84 ASN cc_start: 0.8852 (m110) cc_final: 0.8448 (m-40) REVERT: H 86 ARG cc_start: 0.9338 (tpp80) cc_final: 0.8937 (tpp80) REVERT: K 54 GLN cc_start: 0.9329 (pp30) cc_final: 0.8896 (pm20) REVERT: M 104 MET cc_start: 0.8867 (mmm) cc_final: 0.8641 (mmm) REVERT: N 37 ILE cc_start: 0.7625 (pt) cc_final: 0.7394 (pt) REVERT: N 38 MET cc_start: 0.3294 (ppp) cc_final: 0.2891 (ppp) REVERT: N 140 GLU cc_start: 0.9206 (pt0) cc_final: 0.8921 (pt0) outliers start: 41 outliers final: 24 residues processed: 451 average time/residue: 0.1572 time to fit residues: 97.3022 Evaluate side-chains 448 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 420 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 50 ILE 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 38 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 63 GLU 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 93 GLN 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 K residue 55 LYS Chi-restraints excluded: chain N residue 103 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 17 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 118 optimal weight: 0.0060 chunk 89 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 124 optimal weight: 0.0040 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.6012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN E 93 GLN E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.053135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.042711 restraints weight = 92887.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.043938 restraints weight = 43859.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.044744 restraints weight = 26753.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.045339 restraints weight = 18891.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.045759 restraints weight = 14923.102| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 15436 Z= 0.170 Angle : 0.826 14.596 22114 Z= 0.425 Chirality : 0.042 0.383 2519 Planarity : 0.005 0.048 1788 Dihedral : 29.640 172.053 4403 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.61 % Favored : 95.29 % Rotamer: Outliers : 2.96 % Allowed : 35.93 % Favored : 61.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.26), residues: 1062 helix: 0.82 (0.20), residues: 672 sheet: 0.59 (1.26), residues: 24 loop : -0.88 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 136 TYR 0.052 0.002 TYR H 83 PHE 0.051 0.002 PHE E 67 TRP 0.002 0.000 TRP N 141 HIS 0.005 0.001 HIS K 41 Details of bonding type rmsd covalent geometry : bond 0.00377 (15420) covalent geometry : angle 0.80149 (22096) hydrogen bonds : bond 0.04242 ( 872) hydrogen bonds : angle 3.71245 ( 2220) metal coordination : bond 0.02447 ( 16) metal coordination : angle 7.03433 ( 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 476 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 449 time to evaluate : 0.432 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 41 TYR cc_start: 0.8542 (m-80) cc_final: 0.8206 (m-80) REVERT: A 67 PHE cc_start: 0.9314 (t80) cc_final: 0.8961 (t80) REVERT: A 85 GLN cc_start: 0.8559 (mt0) cc_final: 0.8275 (mp10) REVERT: A 93 GLN cc_start: 0.9283 (tp40) cc_final: 0.9034 (tp40) REVERT: A 94 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8400 (mt-10) REVERT: A 129 ARG cc_start: 0.8994 (tpm170) cc_final: 0.8529 (tpm170) REVERT: B 24 ASP cc_start: 0.8396 (t0) cc_final: 0.8128 (t0) REVERT: B 61 PHE cc_start: 0.9114 (t80) cc_final: 0.8862 (t80) REVERT: B 63 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8458 (pm20) REVERT: B 79 LYS cc_start: 0.9082 (mtmt) cc_final: 0.8636 (ptpt) REVERT: C 23 LEU cc_start: 0.9215 (mm) cc_final: 0.8743 (tp) REVERT: C 27 VAL cc_start: 0.9115 (m) cc_final: 0.8525 (p) REVERT: C 56 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8970 (mt-10) REVERT: C 64 GLU cc_start: 0.9284 (tm-30) cc_final: 0.9003 (pp20) REVERT: C 68 ASN cc_start: 0.9258 (m110) cc_final: 0.8381 (m-40) REVERT: C 74 LYS cc_start: 0.9290 (mmmm) cc_final: 0.9059 (mmmt) REVERT: C 75 LYS cc_start: 0.8711 (mmmm) cc_final: 0.8325 (mmmm) REVERT: C 84 GLN cc_start: 0.9386 (tp-100) cc_final: 0.8817 (tm-30) REVERT: C 95 LYS cc_start: 0.9328 (tttp) cc_final: 0.9109 (tptp) REVERT: C 101 THR cc_start: 0.8702 (m) cc_final: 0.8199 (p) REVERT: C 104 GLN cc_start: 0.8511 (mp10) cc_final: 0.8289 (mp10) REVERT: D 47 GLN cc_start: 0.9355 (tm-30) cc_final: 0.9011 (tm-30) REVERT: D 68 ASP cc_start: 0.9463 (t0) cc_final: 0.9075 (t0) REVERT: D 80 LEU cc_start: 0.9632 (tp) cc_final: 0.9276 (tp) REVERT: D 93 GLU cc_start: 0.9003 (pm20) cc_final: 0.8719 (pm20) REVERT: D 96 THR cc_start: 0.9544 (m) cc_final: 0.9303 (p) REVERT: D 120 LYS cc_start: 0.9385 (ttpp) cc_final: 0.9080 (ttpp) REVERT: E 105 GLU cc_start: 0.8801 (pp20) cc_final: 0.8355 (pp20) REVERT: E 120 MET cc_start: 0.8544 (mmm) cc_final: 0.8057 (mmm) REVERT: E 122 LYS cc_start: 0.9281 (ptmt) cc_final: 0.8988 (ptmt) REVERT: E 125 GLN cc_start: 0.9465 (mt0) cc_final: 0.9116 (mp10) REVERT: F 35 ARG cc_start: 0.9265 (ttm-80) cc_final: 0.8953 (ttm-80) REVERT: F 39 ARG cc_start: 0.9278 (mmm-85) cc_final: 0.9039 (mmm-85) REVERT: F 44 LYS cc_start: 0.9377 (tptm) cc_final: 0.8972 (mmmt) REVERT: F 78 ARG cc_start: 0.8414 (ttp80) cc_final: 0.8078 (ttp80) REVERT: F 79 LYS cc_start: 0.8920 (mtpp) cc_final: 0.8470 (mtmm) REVERT: F 93 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8549 (mp10) REVERT: G 32 ARG cc_start: 0.9387 (ttp80) cc_final: 0.9032 (tmm-80) REVERT: G 35 ARG cc_start: 0.8896 (mtm110) cc_final: 0.8478 (mtm-85) REVERT: G 38 ASN cc_start: 0.9087 (m-40) cc_final: 0.8824 (t0) REVERT: G 42 ARG cc_start: 0.8792 (ptp-110) cc_final: 0.8108 (ptm-80) REVERT: G 57 TYR cc_start: 0.9179 (t80) cc_final: 0.8489 (t80) REVERT: G 61 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8754 (mt-10) REVERT: G 75 LYS cc_start: 0.9074 (mmtt) cc_final: 0.8870 (mmtm) REVERT: G 81 ARG cc_start: 0.9185 (tpt170) cc_final: 0.8933 (tpt170) REVERT: H 33 ARG cc_start: 0.8606 (tpp80) cc_final: 0.8265 (tpt170) REVERT: H 37 TYR cc_start: 0.9339 (m-80) cc_final: 0.9107 (m-80) REVERT: H 40 TYR cc_start: 0.9266 (m-80) cc_final: 0.8997 (m-80) REVERT: H 47 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8785 (tm-30) REVERT: H 70 PHE cc_start: 0.9339 (t80) cc_final: 0.9054 (t80) REVERT: H 84 ASN cc_start: 0.8788 (m110) cc_final: 0.8441 (m-40) REVERT: H 86 ARG cc_start: 0.9311 (tpp80) cc_final: 0.8829 (tpp80) REVERT: K 54 GLN cc_start: 0.9319 (pp30) cc_final: 0.8830 (pm20) REVERT: K 66 ASN cc_start: 0.9066 (t0) cc_final: 0.8771 (m-40) REVERT: K 71 ARG cc_start: 0.8198 (tmm-80) cc_final: 0.6953 (tmm-80) REVERT: N 29 ASP cc_start: 0.6659 (t70) cc_final: 0.6003 (p0) REVERT: N 38 MET cc_start: 0.3310 (ppp) cc_final: 0.2925 (ppp) REVERT: N 79 ASN cc_start: 0.6424 (m-40) cc_final: 0.5746 (p0) REVERT: N 140 GLU cc_start: 0.9099 (pt0) cc_final: 0.8871 (pt0) outliers start: 27 outliers final: 17 residues processed: 457 average time/residue: 0.1596 time to fit residues: 99.9144 Evaluate side-chains 434 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 415 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 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 62 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 63 GLU 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 93 GLN 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 95 GLN Chi-restraints excluded: chain N residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 94 optimal weight: 6.9990 chunk 26 optimal weight: 40.0000 chunk 7 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 69 optimal weight: 0.3980 chunk 79 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.050852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.040478 restraints weight = 95427.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.041678 restraints weight = 45194.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.042452 restraints weight = 27460.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.043005 restraints weight = 19495.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.043387 restraints weight = 15563.561| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 15436 Z= 0.238 Angle : 0.860 18.603 22114 Z= 0.446 Chirality : 0.045 0.411 2519 Planarity : 0.006 0.133 1788 Dihedral : 29.779 171.945 4403 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.39 % Rotamer: Outliers : 2.96 % Allowed : 36.80 % Favored : 60.24 % 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 aren not related in a simple way. whole: 0.14 (0.25), residues: 1062 helix: 0.67 (0.19), residues: 671 sheet: 0.31 (1.18), residues: 24 loop : -0.88 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 136 TYR 0.050 0.003 TYR B 88 PHE 0.048 0.002 PHE E 67 TRP 0.004 0.001 TRP N 141 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00544 (15420) covalent geometry : angle 0.82897 (22096) hydrogen bonds : bond 0.05036 ( 872) hydrogen bonds : angle 3.94358 ( 2220) metal coordination : bond 0.02285 ( 16) metal coordination : angle 8.03309 ( 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 445 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 418 time to evaluate : 0.438 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 85 GLN cc_start: 0.8729 (mt0) cc_final: 0.8364 (mp10) REVERT: A 93 GLN cc_start: 0.9350 (tp40) cc_final: 0.8969 (tp40) REVERT: A 94 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8807 (mm-30) REVERT: A 112 ILE cc_start: 0.9496 (pt) cc_final: 0.9162 (mt) REVERT: A 129 ARG cc_start: 0.9029 (tpm170) cc_final: 0.8560 (tpm170) REVERT: B 24 ASP cc_start: 0.8492 (t0) cc_final: 0.8177 (t0) REVERT: B 63 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8389 (pm20) REVERT: B 88 TYR cc_start: 0.9001 (m-80) cc_final: 0.8622 (m-80) REVERT: C 23 LEU cc_start: 0.9237 (mm) cc_final: 0.8805 (tp) REVERT: C 64 GLU cc_start: 0.9291 (tm-30) cc_final: 0.8957 (pp20) REVERT: C 68 ASN cc_start: 0.9033 (m110) cc_final: 0.8700 (m110) REVERT: C 74 LYS cc_start: 0.9275 (mmmm) cc_final: 0.9039 (mmmt) REVERT: C 75 LYS cc_start: 0.8692 (mmmm) cc_final: 0.8351 (mmmm) REVERT: C 84 GLN cc_start: 0.9447 (tp-100) cc_final: 0.8833 (tm-30) REVERT: C 95 LYS cc_start: 0.9364 (tttp) cc_final: 0.9140 (tptp) REVERT: C 101 THR cc_start: 0.8791 (m) cc_final: 0.8286 (p) REVERT: D 47 GLN cc_start: 0.9364 (tm-30) cc_final: 0.9022 (tm-30) REVERT: D 68 ASP cc_start: 0.9501 (t0) cc_final: 0.9245 (t0) REVERT: D 80 LEU cc_start: 0.9671 (tp) cc_final: 0.9429 (tp) REVERT: D 93 GLU cc_start: 0.9012 (pm20) cc_final: 0.8736 (pm20) REVERT: D 96 THR cc_start: 0.9577 (m) cc_final: 0.9256 (p) REVERT: D 108 LYS cc_start: 0.9528 (ptmt) cc_final: 0.9177 (pttp) REVERT: D 120 LYS cc_start: 0.9387 (ttpp) cc_final: 0.9077 (ttpp) REVERT: E 79 LYS cc_start: 0.9374 (tptp) cc_final: 0.8999 (tptp) REVERT: E 105 GLU cc_start: 0.8786 (pp20) cc_final: 0.8317 (pp20) REVERT: E 120 MET cc_start: 0.8537 (mmm) cc_final: 0.8016 (mmm) REVERT: E 125 GLN cc_start: 0.9467 (mt0) cc_final: 0.9119 (mp10) REVERT: E 133 GLU cc_start: 0.8478 (mp0) cc_final: 0.7992 (mt-10) REVERT: F 31 LYS cc_start: 0.9539 (tmtm) cc_final: 0.9223 (tmtm) REVERT: F 44 LYS cc_start: 0.9438 (tptm) cc_final: 0.9006 (mmmm) REVERT: F 79 LYS cc_start: 0.9050 (mtpp) cc_final: 0.8613 (mtmm) REVERT: F 84 MET cc_start: 0.8625 (mmm) cc_final: 0.8346 (tpp) REVERT: F 93 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8605 (mp10) REVERT: G 32 ARG cc_start: 0.9345 (ttp80) cc_final: 0.8968 (tmm-80) REVERT: G 35 ARG cc_start: 0.8888 (mtm110) cc_final: 0.8525 (mtm-85) REVERT: G 36 LYS cc_start: 0.9348 (mtpt) cc_final: 0.9044 (mtmm) REVERT: G 38 ASN cc_start: 0.9212 (m-40) cc_final: 0.8753 (t0) REVERT: G 42 ARG cc_start: 0.8780 (ptp-110) cc_final: 0.7977 (ptm160) REVERT: G 81 ARG cc_start: 0.9165 (tpt170) cc_final: 0.8684 (tpt170) REVERT: H 33 ARG cc_start: 0.8679 (tpp80) cc_final: 0.8333 (tpp80) REVERT: H 37 TYR cc_start: 0.9431 (m-80) cc_final: 0.9221 (m-80) REVERT: H 40 TYR cc_start: 0.9344 (m-80) cc_final: 0.8937 (m-80) REVERT: H 47 GLN cc_start: 0.9098 (tm-30) cc_final: 0.8801 (tm-30) REVERT: H 84 ASN cc_start: 0.8879 (m110) cc_final: 0.8454 (m-40) REVERT: H 86 ARG cc_start: 0.9323 (tpp80) cc_final: 0.8802 (tpp80) REVERT: K 54 GLN cc_start: 0.9300 (pp30) cc_final: 0.8882 (pm20) REVERT: N 33 TRP cc_start: 0.8706 (m-10) cc_final: 0.8458 (m-10) REVERT: N 38 MET cc_start: 0.3436 (ppp) cc_final: 0.3169 (ppp) REVERT: N 79 ASN cc_start: 0.6683 (m-40) cc_final: 0.5864 (p0) REVERT: N 140 GLU cc_start: 0.9104 (pt0) cc_final: 0.8871 (pt0) REVERT: N 147 MET cc_start: 0.7900 (mtm) cc_final: 0.7570 (mpp) outliers start: 27 outliers final: 18 residues processed: 426 average time/residue: 0.1635 time to fit residues: 95.0049 Evaluate side-chains 427 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 407 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 82 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 E residue 57 SER Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 63 GLU 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 87 VAL Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain K residue 55 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 113 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 105 optimal weight: 20.0000 chunk 8 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 93 GLN ** K 54 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** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.052530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.042094 restraints weight = 93000.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.043299 restraints weight = 44066.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.044138 restraints weight = 26949.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.044711 restraints weight = 18960.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.045118 restraints weight = 14983.926| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 15436 Z= 0.179 Angle : 0.848 16.426 22114 Z= 0.437 Chirality : 0.043 0.389 2519 Planarity : 0.006 0.111 1788 Dihedral : 29.716 171.758 4403 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.90 % Favored : 95.01 % Rotamer: Outliers : 2.63 % Allowed : 38.01 % Favored : 59.36 % 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 aren not related in a simple way. whole: 0.05 (0.25), residues: 1062 helix: 0.58 (0.19), residues: 672 sheet: 0.92 (1.21), residues: 23 loop : -0.92 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 136 TYR 0.042 0.002 TYR B 88 PHE 0.047 0.003 PHE E 67 TRP 0.003 0.001 TRP N 93 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00403 (15420) covalent geometry : angle 0.82290 (22096) hydrogen bonds : bond 0.04338 ( 872) hydrogen bonds : angle 3.85828 ( 2220) metal coordination : bond 0.02399 ( 16) metal coordination : angle 7.24663 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2747.42 seconds wall clock time: 48 minutes 11.23 seconds (2891.23 seconds total)