Starting phenix.real_space_refine on Fri Jun 13 18:16:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8grq_34212/06_2025/8grq_34212.cif Found real_map, /net/cci-nas-00/data/ceres_data/8grq_34212/06_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_34212/06_2025/8grq_34212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8grq_34212/06_2025/8grq_34212.map" model { file = "/net/cci-nas-00/data/ceres_data/8grq_34212/06_2025/8grq_34212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8grq_34212/06_2025/8grq_34212.cif" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'TRP:plan': 2, '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: 9.04, per 1000 atoms: 0.62 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: 3.94 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 8.28 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: 5.66 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3605 1.34 - 1.46: 4658 1.46 - 1.58: 6518 1.58 - 1.70: 586 1.70 - 1.82: 53 Bond restraints: 15420 Sorted by residual: bond pdb=" 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 44.220 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.280 ------------------------------------------------------------------------------- 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 : 14.63 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP N 93 HIS 0.005 0.001 HIS C 82 PHE 0.013 0.001 PHE K 79 TYR 0.020 0.002 TYR B 88 ARG 0.007 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.14169 ( 872) hydrogen bonds : angle 5.32690 ( 2220) metal coordination : bond 0.03062 ( 16) metal coordination : angle 6.26842 ( 18) covalent geometry : bond 0.00371 (15420) covalent geometry : angle 0.66945 (22096) *********************** 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 : 1.202 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: 0.3585 time to fit residues: 253.5391 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 : 1.113 ------------------------------------------------------------------------------- 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 110 optimal weight: 50.0000 chunk 99 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 53 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 C 104 GLN D 109 HIS E 68 GLN G 31 HIS ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 143 GLN ** 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 = 0.3156 r_free = 0.3156 target = 0.049748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.039239 restraints weight = 95178.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.040460 restraints weight = 43713.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.041306 restraints weight = 26454.116| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 15436 Z= 0.327 Angle : 0.776 18.089 22114 Z= 0.422 Chirality : 0.044 0.206 2519 Planarity : 0.005 0.046 1788 Dihedral : 29.277 169.754 4404 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.48 % Favored : 96.42 % Rotamer: Outliers : 5.81 % Allowed : 19.61 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1062 helix: 1.13 (0.20), residues: 668 sheet: 0.74 (1.19), residues: 24 loop : -0.88 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 33 HIS 0.009 0.002 HIS F 75 PHE 0.032 0.002 PHE F 61 TYR 0.043 0.003 TYR D 83 ARG 0.009 0.001 ARG C 42 Details of bonding type rmsd hydrogen bonds : bond 0.06425 ( 872) hydrogen bonds : angle 4.04486 ( 2220) metal coordination : bond 0.02799 ( 16) metal coordination : angle 8.17592 ( 18) covalent geometry : bond 0.00735 (15420) covalent geometry : angle 0.74075 (22096) *********************** 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 495 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 442 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9642 (t80) cc_final: 0.9400 (t80) REVERT: A 80 THR cc_start: 0.9398 (OUTLIER) cc_final: 0.9135 (p) REVERT: A 85 GLN cc_start: 0.8900 (mt0) cc_final: 0.8669 (mt0) REVERT: A 94 GLU cc_start: 0.9334 (mm-30) cc_final: 0.8930 (mm-30) REVERT: A 105 GLU cc_start: 0.9036 (tp30) cc_final: 0.8615 (tp30) REVERT: A 109 LEU cc_start: 0.9388 (mp) cc_final: 0.8463 (mp) REVERT: A 129 ARG cc_start: 0.8821 (tpm170) cc_final: 0.8531 (tpm170) REVERT: B 49 LEU cc_start: 0.9026 (mm) cc_final: 0.8714 (mt) REVERT: B 52 GLU cc_start: 0.8410 (pm20) cc_final: 0.7822 (pm20) REVERT: C 23 LEU cc_start: 0.9073 (mt) cc_final: 0.8826 (mt) REVERT: C 38 ASN cc_start: 0.9037 (m-40) cc_final: 0.8587 (p0) REVERT: C 54 VAL cc_start: 0.9697 (OUTLIER) cc_final: 0.9465 (p) REVERT: C 101 THR cc_start: 0.9200 (m) cc_final: 0.8682 (p) REVERT: C 104 GLN cc_start: 0.8329 (mp10) cc_final: 0.8043 (mp10) REVERT: C 115 LEU cc_start: 0.9303 (mt) cc_final: 0.9053 (mt) REVERT: D 35 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6972 (mm-30) REVERT: D 68 ASP cc_start: 0.9375 (t0) cc_final: 0.9048 (t0) REVERT: D 88 THR cc_start: 0.9586 (m) cc_final: 0.9353 (p) REVERT: D 89 ILE cc_start: 0.9059 (mm) cc_final: 0.8778 (mm) REVERT: D 93 GLU cc_start: 0.9110 (pm20) cc_final: 0.8718 (pm20) REVERT: D 96 THR cc_start: 0.9598 (m) cc_final: 0.9329 (p) REVERT: D 105 GLU cc_start: 0.8314 (pm20) cc_final: 0.7967 (pm20) REVERT: E 50 GLU cc_start: 0.9413 (pt0) cc_final: 0.8814 (pt0) REVERT: E 90 MET cc_start: 0.8963 (mmp) cc_final: 0.8730 (mmm) REVERT: E 120 MET cc_start: 0.8486 (mmm) cc_final: 0.8238 (mmm) REVERT: E 122 LYS cc_start: 0.9211 (ptmt) cc_final: 0.8929 (ptmt) REVERT: E 125 GLN cc_start: 0.9479 (mt0) cc_final: 0.9125 (mp10) REVERT: E 133 GLU cc_start: 0.8013 (mp0) cc_final: 0.7759 (mp0) REVERT: F 35 ARG cc_start: 0.9424 (mtp-110) cc_final: 0.9179 (ttm-80) REVERT: F 39 ARG cc_start: 0.9323 (mmt90) cc_final: 0.8694 (mmt90) REVERT: F 49 LEU cc_start: 0.9273 (mt) cc_final: 0.8915 (mm) REVERT: F 79 LYS cc_start: 0.9126 (mtpp) cc_final: 0.8869 (mtmm) REVERT: F 84 MET cc_start: 0.8905 (mmm) cc_final: 0.8640 (mmm) REVERT: F 88 TYR cc_start: 0.9346 (m-10) cc_final: 0.8961 (m-80) REVERT: F 95 ARG cc_start: 0.8933 (mtp85) cc_final: 0.8689 (mtt90) REVERT: G 32 ARG cc_start: 0.9270 (ttp80) cc_final: 0.9018 (ttp80) REVERT: G 38 ASN cc_start: 0.9304 (m-40) cc_final: 0.9070 (m-40) REVERT: G 57 TYR cc_start: 0.9296 (t80) cc_final: 0.9092 (t80) REVERT: G 75 LYS cc_start: 0.9387 (mttm) cc_final: 0.9155 (mmmm) REVERT: H 37 TYR cc_start: 0.9470 (m-80) cc_final: 0.9193 (m-80) REVERT: H 40 TYR cc_start: 0.9468 (m-80) cc_final: 0.8800 (m-80) REVERT: H 47 GLN cc_start: 0.8953 (tm-30) cc_final: 0.8743 (tm-30) REVERT: H 86 ARG cc_start: 0.9372 (tpp80) cc_final: 0.9008 (tpp80) REVERT: H 106 LEU cc_start: 0.9280 (mt) cc_final: 0.9025 (mt) REVERT: K 50 LYS cc_start: 0.9232 (mptt) cc_final: 0.9020 (mptt) REVERT: K 79 PHE cc_start: 0.8882 (t80) cc_final: 0.8681 (t80) REVERT: M 77 ASP cc_start: 0.8244 (m-30) cc_final: 0.7550 (p0) REVERT: M 104 MET cc_start: 0.8995 (mmm) cc_final: 0.8697 (mmm) REVERT: N 38 MET cc_start: 0.3361 (ppp) cc_final: 0.3150 (ppp) REVERT: N 79 ASN cc_start: 0.6523 (p0) cc_final: 0.6209 (p0) outliers start: 53 outliers final: 38 residues processed: 461 average time/residue: 0.3158 time to fit residues: 198.5524 Evaluate side-chains 448 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 408 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 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 67 ASN Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain 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 20 optimal weight: 0.3980 chunk 120 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 7 optimal weight: 0.3980 chunk 5 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 9 optimal weight: 0.1980 chunk 87 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS C 94 ASN E 68 GLN E 85 GLN G 68 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 ASN ** K 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 143 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.052474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.041865 restraints weight = 91601.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.043137 restraints weight = 41731.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.044025 restraints weight = 25130.491| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 15436 Z= 0.165 Angle : 0.707 13.602 22114 Z= 0.382 Chirality : 0.040 0.308 2519 Planarity : 0.004 0.042 1788 Dihedral : 29.318 171.364 4403 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.48 % Favored : 96.42 % Rotamer: Outliers : 3.72 % Allowed : 24.10 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1062 helix: 1.15 (0.20), residues: 664 sheet: 0.69 (1.19), residues: 24 loop : -0.96 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 141 HIS 0.005 0.001 HIS F 75 PHE 0.031 0.002 PHE E 67 TYR 0.029 0.002 TYR D 83 ARG 0.007 0.001 ARG N 139 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 872) hydrogen bonds : angle 3.58335 ( 2220) metal coordination : bond 0.02750 ( 16) metal coordination : angle 6.94800 ( 18) covalent geometry : bond 0.00363 (15420) covalent geometry : angle 0.67858 (22096) *********************** 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 504 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 470 time to evaluate : 1.374 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: 0.8904 (tp40) cc_final: 0.7743 (tp40) REVERT: A 105 GLU cc_start: 0.8997 (tp30) cc_final: 0.8792 (tp30) REVERT: A 109 LEU cc_start: 0.9388 (mp) cc_final: 0.8910 (mp) REVERT: A 120 MET cc_start: 0.8335 (mmm) cc_final: 0.7942 (mtp) REVERT: A 129 ARG cc_start: 0.8863 (tpm170) cc_final: 0.8489 (tpm170) REVERT: B 24 ASP cc_start: 0.7809 (t0) cc_final: 0.7483 (t0) REVERT: B 49 LEU cc_start: 0.8912 (mm) cc_final: 0.8628 (tp) REVERT: B 79 LYS cc_start: 0.9060 (mtmt) cc_final: 0.8655 (ptpt) REVERT: B 88 TYR cc_start: 0.9007 (m-80) cc_final: 0.8671 (m-80) REVERT: C 38 ASN cc_start: 0.8908 (m-40) cc_final: 0.8544 (p0) REVERT: C 56 GLU cc_start: 0.9302 (mt-10) cc_final: 0.9095 (mt-10) REVERT: C 68 ASN cc_start: 0.9146 (m110) cc_final: 0.8880 (m110) REVERT: C 75 LYS cc_start: 0.8632 (mmmm) cc_final: 0.8416 (mmmm) REVERT: C 95 LYS cc_start: 0.9399 (tttm) cc_final: 0.9158 (tptp) REVERT: C 101 THR cc_start: 0.9084 (m) cc_final: 0.8596 (p) REVERT: D 68 ASP cc_start: 0.9399 (t0) cc_final: 0.9089 (t0) REVERT: D 71 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8756 (tm-30) REVERT: D 89 ILE cc_start: 0.8931 (mm) cc_final: 0.8682 (mm) REVERT: D 93 GLU cc_start: 0.8920 (pm20) cc_final: 0.8534 (pm20) REVERT: D 96 THR cc_start: 0.9558 (m) cc_final: 0.9326 (p) REVERT: E 50 GLU cc_start: 0.9450 (pt0) cc_final: 0.9051 (pt0) REVERT: E 60 LEU cc_start: 0.9349 (mm) cc_final: 0.9088 (mm) REVERT: E 120 MET cc_start: 0.8532 (mmm) cc_final: 0.8178 (mmm) REVERT: E 125 GLN cc_start: 0.9476 (mt0) cc_final: 0.9074 (mp10) REVERT: E 133 GLU cc_start: 0.8024 (mp0) cc_final: 0.7801 (mp0) REVERT: F 31 LYS cc_start: 0.9602 (tttp) cc_final: 0.9320 (tttm) REVERT: F 39 ARG cc_start: 0.9359 (mmt90) cc_final: 0.8987 (mmt90) REVERT: F 44 LYS cc_start: 0.9327 (tptm) cc_final: 0.9055 (tppp) REVERT: F 79 LYS cc_start: 0.9065 (mtpp) cc_final: 0.8725 (mtmm) REVERT: F 84 MET cc_start: 0.8900 (mmm) cc_final: 0.8660 (mmm) REVERT: F 88 TYR cc_start: 0.9303 (m-10) cc_final: 0.8278 (m-10) REVERT: F 92 ARG cc_start: 0.9377 (mtp-110) cc_final: 0.9072 (ttt-90) REVERT: F 95 ARG cc_start: 0.8837 (mtp85) cc_final: 0.8519 (mtt90) REVERT: G 32 ARG cc_start: 0.9365 (ttp80) cc_final: 0.8700 (ttp80) REVERT: G 35 ARG cc_start: 0.8817 (mtm110) cc_final: 0.8408 (mtp-110) REVERT: G 36 LYS cc_start: 0.9187 (mmtm) cc_final: 0.8434 (mmtm) REVERT: G 39 TYR cc_start: 0.9228 (m-80) cc_final: 0.8918 (m-80) REVERT: G 42 ARG cc_start: 0.8707 (ptp-110) cc_final: 0.8042 (ptm-80) REVERT: G 81 ARG cc_start: 0.9233 (tpt90) cc_final: 0.8870 (tpt170) REVERT: H 33 ARG cc_start: 0.8427 (tpp80) cc_final: 0.8195 (tpp80) REVERT: H 37 TYR cc_start: 0.9435 (m-80) cc_final: 0.9053 (m-80) REVERT: H 47 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8640 (tm-30) REVERT: H 68 ASP cc_start: 0.9260 (t0) cc_final: 0.8994 (t0) REVERT: H 70 PHE cc_start: 0.9352 (t80) cc_final: 0.9090 (t80) REVERT: H 84 ASN cc_start: 0.9082 (m110) cc_final: 0.8695 (m110) REVERT: H 86 ARG cc_start: 0.9368 (tpp80) cc_final: 0.8852 (tpp80) REVERT: H 92 ARG cc_start: 0.8941 (mtp-110) cc_final: 0.8317 (ttp80) REVERT: K 51 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9010 (tp) REVERT: K 54 GLN cc_start: 0.9284 (pp30) cc_final: 0.9058 (pp30) REVERT: N 38 MET cc_start: 0.3854 (ppp) cc_final: 0.3469 (ppp) REVERT: N 147 MET cc_start: 0.7618 (ptp) cc_final: 0.7345 (mpp) outliers start: 34 outliers final: 20 residues processed: 479 average time/residue: 0.3843 time to fit residues: 253.6341 Evaluate side-chains 440 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 419 time to evaluate : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP 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 C residue 76 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 87 VAL 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 90 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain N residue 37 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 116 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 124 optimal weight: 50.0000 chunk 127 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 61 optimal weight: 0.0070 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.5804 ------------------------------------------------------------------------------- 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** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN C 94 ASN E 68 GLN F 27 GLN G 31 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.051374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.040870 restraints weight = 93530.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.042107 restraints weight = 43381.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.042938 restraints weight = 26006.302| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 15436 Z= 0.213 Angle : 0.730 15.350 22114 Z= 0.391 Chirality : 0.040 0.276 2519 Planarity : 0.005 0.068 1788 Dihedral : 29.412 171.506 4403 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 5.59 % Allowed : 26.29 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1062 helix: 1.15 (0.20), residues: 668 sheet: 0.74 (1.20), residues: 24 loop : -0.93 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 141 HIS 0.004 0.001 HIS F 75 PHE 0.025 0.002 PHE F 61 TYR 0.027 0.002 TYR C 39 ARG 0.007 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.04628 ( 872) hydrogen bonds : angle 3.64865 ( 2220) metal coordination : bond 0.02592 ( 16) metal coordination : angle 7.51620 ( 18) covalent geometry : bond 0.00484 (15420) covalent geometry : angle 0.69829 (22096) *********************** 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: 51 poor density : 438 time to evaluate : 1.145 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: 0.8453 (m-80) cc_final: 0.7949 (m-80) REVERT: A 94 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8750 (mm-30) REVERT: A 112 ILE cc_start: 0.9384 (pt) cc_final: 0.9126 (mt) REVERT: A 120 MET cc_start: 0.8468 (mmm) cc_final: 0.7953 (mtp) REVERT: A 129 ARG cc_start: 0.8882 (tpm170) cc_final: 0.8461 (tpm170) REVERT: B 24 ASP cc_start: 0.7798 (t0) cc_final: 0.7469 (t0) REVERT: B 49 LEU cc_start: 0.9003 (mm) cc_final: 0.8705 (tp) REVERT: B 63 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8584 (pm20) REVERT: B 79 LYS cc_start: 0.9100 (mtmt) cc_final: 0.8673 (ptpt) REVERT: B 88 TYR cc_start: 0.9103 (m-10) cc_final: 0.8291 (m-80) REVERT: C 38 ASN cc_start: 0.8879 (m-40) cc_final: 0.8448 (m-40) REVERT: C 56 GLU cc_start: 0.9325 (mt-10) cc_final: 0.9015 (mt-10) REVERT: C 68 ASN cc_start: 0.9161 (m-40) cc_final: 0.8795 (m110) REVERT: C 75 LYS cc_start: 0.8663 (mmmm) cc_final: 0.8449 (mmmm) REVERT: C 95 LYS cc_start: 0.9407 (tttp) cc_final: 0.9167 (tptp) REVERT: C 101 THR cc_start: 0.9083 (m) cc_final: 0.8627 (p) REVERT: C 104 GLN cc_start: 0.8191 (mp10) cc_final: 0.7806 (mp-120) REVERT: D 47 GLN cc_start: 0.9290 (tm-30) cc_final: 0.8948 (tm-30) REVERT: D 68 ASP cc_start: 0.9430 (t0) cc_final: 0.9139 (t0) REVERT: D 83 TYR cc_start: 0.7887 (m-10) cc_final: 0.6537 (m-10) REVERT: D 96 THR cc_start: 0.9568 (m) cc_final: 0.9321 (p) REVERT: D 105 GLU cc_start: 0.8163 (pm20) cc_final: 0.7515 (pm20) REVERT: D 108 LYS cc_start: 0.9426 (ptpp) cc_final: 0.9120 (pttp) REVERT: E 50 GLU cc_start: 0.9380 (pt0) cc_final: 0.9146 (pt0) REVERT: E 120 MET cc_start: 0.8568 (mmm) cc_final: 0.8167 (mmm) REVERT: E 125 GLN cc_start: 0.9473 (mt0) cc_final: 0.9114 (mp10) REVERT: E 133 GLU cc_start: 0.8097 (mp0) cc_final: 0.7883 (mp0) REVERT: F 27 GLN cc_start: 0.9212 (mm-40) cc_final: 0.8746 (mp10) REVERT: F 35 ARG cc_start: 0.9324 (ttm-80) cc_final: 0.8728 (ttm-80) REVERT: F 44 LYS cc_start: 0.9398 (tptm) cc_final: 0.9128 (tppp) REVERT: F 79 LYS cc_start: 0.9009 (mtpp) cc_final: 0.8773 (mtmm) REVERT: F 84 MET cc_start: 0.8820 (mmm) cc_final: 0.8516 (mmm) REVERT: F 88 TYR cc_start: 0.9195 (m-10) cc_final: 0.8830 (m-10) REVERT: F 95 ARG cc_start: 0.8812 (mtp85) cc_final: 0.8517 (mtt90) REVERT: G 32 ARG cc_start: 0.9372 (ttp80) cc_final: 0.8878 (ttp80) REVERT: G 36 LYS cc_start: 0.9253 (mmtm) cc_final: 0.8809 (mmtm) REVERT: G 38 ASN cc_start: 0.9240 (m-40) cc_final: 0.8935 (t0) REVERT: G 42 ARG cc_start: 0.8752 (ptp-110) cc_final: 0.8062 (ptm-80) REVERT: G 81 ARG cc_start: 0.9225 (tpt170) cc_final: 0.8963 (tpt170) REVERT: H 33 ARG cc_start: 0.8536 (tpp80) cc_final: 0.8331 (tpp80) REVERT: H 37 TYR cc_start: 0.9438 (m-80) cc_final: 0.9053 (m-80) REVERT: H 47 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8614 (tm-30) REVERT: H 83 TYR cc_start: 0.8875 (m-10) cc_final: 0.8509 (m-80) REVERT: H 84 ASN cc_start: 0.9097 (m110) cc_final: 0.8681 (m110) REVERT: H 86 ARG cc_start: 0.9342 (tpp80) cc_final: 0.8952 (tpp80) REVERT: M 104 MET cc_start: 0.8899 (mmm) cc_final: 0.8613 (mmm) REVERT: N 38 MET cc_start: 0.3544 (ppp) cc_final: 0.3185 (ppp) REVERT: N 147 MET cc_start: 0.7626 (ptp) cc_final: 0.7339 (mpp) outliers start: 51 outliers final: 32 residues processed: 454 average time/residue: 0.3250 time to fit residues: 202.0397 Evaluate side-chains 432 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 399 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain 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 112 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain N residue 37 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 84 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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** B 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.051711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.041116 restraints weight = 94039.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.042357 restraints weight = 43917.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.043189 restraints weight = 26460.957| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 15436 Z= 0.189 Angle : 0.716 14.727 22114 Z= 0.385 Chirality : 0.040 0.323 2519 Planarity : 0.005 0.042 1788 Dihedral : 29.530 171.964 4403 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 4.82 % Allowed : 28.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.26), residues: 1062 helix: 1.15 (0.20), residues: 668 sheet: 0.77 (1.24), residues: 24 loop : -0.83 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 93 HIS 0.004 0.001 HIS K 41 PHE 0.028 0.002 PHE F 61 TYR 0.023 0.002 TYR D 40 ARG 0.008 0.001 ARG M 112 Details of bonding type rmsd hydrogen bonds : bond 0.04331 ( 872) hydrogen bonds : angle 3.57684 ( 2220) metal coordination : bond 0.02566 ( 16) metal coordination : angle 6.99885 ( 18) covalent geometry : bond 0.00426 (15420) covalent geometry : angle 0.68782 (22096) *********************** 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 471 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 427 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.8435 (m-80) cc_final: 0.8003 (m-80) REVERT: A 94 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8702 (mm-30) REVERT: A 97 GLU cc_start: 0.8163 (mp0) cc_final: 0.7671 (mp0) REVERT: A 120 MET cc_start: 0.8448 (mmm) cc_final: 0.8087 (mtp) REVERT: A 129 ARG cc_start: 0.8923 (tpm170) cc_final: 0.8515 (tpm170) REVERT: B 24 ASP cc_start: 0.7949 (t0) cc_final: 0.7624 (t0) REVERT: B 49 LEU cc_start: 0.8938 (mm) cc_final: 0.8549 (tp) REVERT: B 63 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8570 (pm20) REVERT: B 79 LYS cc_start: 0.9068 (mtmt) cc_final: 0.8649 (ptpt) REVERT: B 88 TYR cc_start: 0.9164 (m-10) cc_final: 0.8873 (m-80) REVERT: C 38 ASN cc_start: 0.8883 (m-40) cc_final: 0.8314 (m-40) REVERT: C 39 TYR cc_start: 0.9372 (m-80) cc_final: 0.8998 (m-80) REVERT: C 56 GLU cc_start: 0.9346 (mt-10) cc_final: 0.9065 (mt-10) REVERT: C 68 ASN cc_start: 0.9261 (m-40) cc_final: 0.9007 (m110) REVERT: C 95 LYS cc_start: 0.9384 (tttp) cc_final: 0.9152 (tptp) REVERT: C 101 THR cc_start: 0.8990 (m) cc_final: 0.8477 (p) REVERT: C 104 GLN cc_start: 0.8316 (mp10) cc_final: 0.8086 (mp10) REVERT: D 47 GLN cc_start: 0.9329 (tm-30) cc_final: 0.8969 (tm-30) REVERT: D 68 ASP cc_start: 0.9420 (t0) cc_final: 0.9190 (t0) REVERT: D 93 GLU cc_start: 0.9160 (pm20) cc_final: 0.8903 (pm20) REVERT: D 96 THR cc_start: 0.9597 (m) cc_final: 0.9327 (p) REVERT: D 105 GLU cc_start: 0.8452 (pm20) cc_final: 0.8137 (pm20) REVERT: D 108 LYS cc_start: 0.9439 (ptpp) cc_final: 0.9147 (pttp) REVERT: E 50 GLU cc_start: 0.9322 (pt0) cc_final: 0.9087 (pt0) REVERT: E 120 MET cc_start: 0.8605 (mmm) cc_final: 0.8166 (mmm) REVERT: E 125 GLN cc_start: 0.9475 (mt0) cc_final: 0.9114 (mp10) REVERT: E 133 GLU cc_start: 0.8115 (mp0) cc_final: 0.7884 (mp0) REVERT: F 27 GLN cc_start: 0.9247 (mm-40) cc_final: 0.8748 (mp10) REVERT: F 35 ARG cc_start: 0.9309 (ttm-80) cc_final: 0.8871 (ttm-80) REVERT: F 44 LYS cc_start: 0.9441 (tptm) cc_final: 0.9150 (tppp) REVERT: F 79 LYS cc_start: 0.9031 (mtpp) cc_final: 0.8657 (mtmm) REVERT: F 84 MET cc_start: 0.8878 (mmm) cc_final: 0.8623 (mmm) REVERT: F 88 TYR cc_start: 0.9316 (m-10) cc_final: 0.8594 (m-10) REVERT: G 32 ARG cc_start: 0.9346 (ttp80) cc_final: 0.8792 (tmm-80) REVERT: G 36 LYS cc_start: 0.9237 (mmtm) cc_final: 0.8768 (mmtm) REVERT: G 38 ASN cc_start: 0.9212 (m-40) cc_final: 0.8872 (t0) REVERT: G 42 ARG cc_start: 0.8743 (ptp-110) cc_final: 0.8075 (ptm-80) REVERT: G 81 ARG cc_start: 0.9163 (tpt170) cc_final: 0.8928 (tpt170) REVERT: H 33 ARG cc_start: 0.8539 (tpp80) cc_final: 0.8267 (tpp80) REVERT: H 37 TYR cc_start: 0.9413 (m-80) cc_final: 0.9073 (m-80) REVERT: H 70 PHE cc_start: 0.9420 (t80) cc_final: 0.9191 (t80) REVERT: H 83 TYR cc_start: 0.8800 (m-10) cc_final: 0.8340 (m-80) REVERT: H 84 ASN cc_start: 0.9074 (m110) cc_final: 0.8700 (m-40) REVERT: H 86 ARG cc_start: 0.9353 (tpp80) cc_final: 0.8940 (tpp80) REVERT: K 43 PHE cc_start: 0.7615 (m-10) cc_final: 0.7214 (m-80) REVERT: M 104 MET cc_start: 0.9026 (mmm) cc_final: 0.8725 (mmm) REVERT: N 29 ASP cc_start: 0.6797 (t70) cc_final: 0.6149 (p0) REVERT: N 38 MET cc_start: 0.3574 (ppp) cc_final: 0.3258 (ppp) REVERT: N 140 GLU cc_start: 0.9208 (pt0) cc_final: 0.8978 (pt0) REVERT: N 147 MET cc_start: 0.7551 (ptp) cc_final: 0.7297 (mpp) outliers start: 44 outliers final: 30 residues processed: 445 average time/residue: 0.3241 time to fit residues: 196.8831 Evaluate side-chains 430 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 399 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 100 LEU 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 112 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 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 71 GLU Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 103 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 72 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 61 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 85 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN E 85 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS ** 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** N 32 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.052475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.041848 restraints weight = 93793.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.043062 restraints weight = 44522.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.043922 restraints weight = 27549.277| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 15436 Z= 0.171 Angle : 0.738 14.852 22114 Z= 0.390 Chirality : 0.040 0.342 2519 Planarity : 0.004 0.042 1788 Dihedral : 29.523 172.366 4403 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.58 % Favored : 96.33 % Rotamer: Outliers : 4.16 % Allowed : 30.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1062 helix: 1.13 (0.20), residues: 668 sheet: 1.17 (1.27), residues: 24 loop : -0.74 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 141 HIS 0.004 0.001 HIS K 41 PHE 0.027 0.002 PHE F 61 TYR 0.020 0.002 TYR D 40 ARG 0.006 0.000 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 872) hydrogen bonds : angle 3.51773 ( 2220) metal coordination : bond 0.02637 ( 16) metal coordination : angle 6.66464 ( 18) covalent geometry : bond 0.00385 (15420) covalent geometry : angle 0.71353 (22096) *********************** 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 464 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 426 time to evaluate : 1.310 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: 0.8427 (m-80) cc_final: 0.8042 (m-80) REVERT: A 93 GLN cc_start: 0.8472 (tp40) cc_final: 0.7531 (tp40) REVERT: A 94 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8715 (mm-30) REVERT: A 97 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: A 120 MET cc_start: 0.8410 (mmm) cc_final: 0.8001 (mtp) REVERT: A 129 ARG cc_start: 0.8921 (tpm170) cc_final: 0.8553 (tpm170) REVERT: B 49 LEU cc_start: 0.8914 (mm) cc_final: 0.8554 (tp) REVERT: B 61 PHE cc_start: 0.9076 (t80) cc_final: 0.8855 (t80) REVERT: B 63 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8536 (pm20) REVERT: B 88 TYR cc_start: 0.9187 (m-10) cc_final: 0.8870 (m-80) REVERT: C 38 ASN cc_start: 0.8883 (m-40) cc_final: 0.8409 (p0) REVERT: C 39 TYR cc_start: 0.9325 (m-80) cc_final: 0.9001 (m-80) REVERT: C 56 GLU cc_start: 0.9335 (mt-10) cc_final: 0.9059 (mt-10) REVERT: C 64 GLU cc_start: 0.9295 (tm-30) cc_final: 0.9068 (tm-30) REVERT: C 68 ASN cc_start: 0.9379 (m-40) cc_final: 0.8977 (m110) REVERT: C 75 LYS cc_start: 0.8559 (mmmm) cc_final: 0.8158 (mmmm) REVERT: C 95 LYS cc_start: 0.9369 (tttp) cc_final: 0.9145 (tptp) REVERT: C 101 THR cc_start: 0.8943 (m) cc_final: 0.8433 (p) REVERT: C 104 GLN cc_start: 0.8472 (mp10) cc_final: 0.8173 (mp-120) REVERT: D 33 ARG cc_start: 0.8695 (tpt170) cc_final: 0.8294 (mmt90) REVERT: D 47 GLN cc_start: 0.9329 (tm-30) cc_final: 0.8998 (tm-30) REVERT: D 68 ASP cc_start: 0.9428 (t0) cc_final: 0.9197 (t0) REVERT: D 80 LEU cc_start: 0.9689 (tp) cc_final: 0.9398 (tp) REVERT: D 93 GLU cc_start: 0.9145 (pm20) cc_final: 0.8593 (pm20) REVERT: D 96 THR cc_start: 0.9586 (m) cc_final: 0.9297 (p) REVERT: D 108 LYS cc_start: 0.9444 (ptpp) cc_final: 0.9190 (pttp) REVERT: E 105 GLU cc_start: 0.8622 (pp20) cc_final: 0.8164 (pp20) REVERT: E 120 MET cc_start: 0.8597 (mmm) cc_final: 0.8159 (mmm) REVERT: E 122 LYS cc_start: 0.9218 (ptmt) cc_final: 0.8834 (ptmt) REVERT: E 125 GLN cc_start: 0.9457 (mt0) cc_final: 0.9090 (mp10) REVERT: F 27 GLN cc_start: 0.9232 (mm-40) cc_final: 0.8708 (mp10) REVERT: F 35 ARG cc_start: 0.9295 (ttm-80) cc_final: 0.8929 (ttm-80) REVERT: F 44 LYS cc_start: 0.9437 (tptm) cc_final: 0.9216 (tppp) REVERT: F 78 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8088 (ttp80) REVERT: F 79 LYS cc_start: 0.8907 (mtpp) cc_final: 0.8496 (mtmm) REVERT: F 84 MET cc_start: 0.8886 (mmm) cc_final: 0.8665 (mmm) REVERT: F 88 TYR cc_start: 0.9336 (m-10) cc_final: 0.8625 (m-10) REVERT: F 95 ARG cc_start: 0.8755 (mtp85) cc_final: 0.8460 (mtt90) REVERT: G 32 ARG cc_start: 0.9341 (ttp80) cc_final: 0.8637 (ttp80) REVERT: G 36 LYS cc_start: 0.9221 (mmtm) cc_final: 0.8727 (mmtm) REVERT: G 38 ASN cc_start: 0.9187 (m-40) cc_final: 0.8895 (t0) REVERT: G 39 TYR cc_start: 0.9175 (m-80) cc_final: 0.8904 (m-80) REVERT: G 42 ARG cc_start: 0.8739 (ptp-110) cc_final: 0.8088 (ptm-80) REVERT: G 57 TYR cc_start: 0.9311 (t80) cc_final: 0.8564 (t80) REVERT: G 61 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8232 (mp0) REVERT: G 81 ARG cc_start: 0.9157 (tpt170) cc_final: 0.8892 (tpt170) REVERT: H 33 ARG cc_start: 0.8607 (tpp80) cc_final: 0.8276 (tpp80) REVERT: H 35 GLU cc_start: 0.8317 (tp30) cc_final: 0.8112 (tp30) REVERT: H 37 TYR cc_start: 0.9392 (m-80) cc_final: 0.9082 (m-80) REVERT: H 83 TYR cc_start: 0.8796 (m-10) cc_final: 0.8329 (m-80) REVERT: H 84 ASN cc_start: 0.9042 (m110) cc_final: 0.8661 (m-40) REVERT: H 86 ARG cc_start: 0.9332 (tpp80) cc_final: 0.8886 (tpp80) REVERT: M 104 MET cc_start: 0.9041 (mmm) cc_final: 0.8744 (mmm) REVERT: N 38 MET cc_start: 0.4197 (ppp) cc_final: 0.3792 (ppp) REVERT: N 140 GLU cc_start: 0.9199 (pt0) cc_final: 0.8895 (pt0) REVERT: N 143 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8458 (mm-40) outliers start: 38 outliers final: 23 residues processed: 442 average time/residue: 0.3339 time to fit residues: 200.2394 Evaluate side-chains 432 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 406 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU 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 D residue 55 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain N residue 31 PHE Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 143 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 18 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.2980 chunk 43 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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** B 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN E 93 GLN ** 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** N 7 ASN N 32 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.053233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.042612 restraints weight = 94215.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.043877 restraints weight = 44574.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.044746 restraints weight = 27167.696| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3820 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= 0.164 Angle : 0.740 13.617 22114 Z= 0.393 Chirality : 0.040 0.376 2519 Planarity : 0.005 0.042 1788 Dihedral : 29.476 173.114 4403 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.67 % Favored : 96.23 % Rotamer: Outliers : 4.16 % Allowed : 31.87 % Favored : 63.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1062 helix: 1.12 (0.20), residues: 673 sheet: 1.13 (1.30), residues: 24 loop : -0.73 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 93 HIS 0.004 0.001 HIS K 41 PHE 0.030 0.002 PHE E 67 TYR 0.017 0.002 TYR B 98 ARG 0.009 0.001 ARG F 39 Details of bonding type rmsd hydrogen bonds : bond 0.04061 ( 872) hydrogen bonds : angle 3.49465 ( 2220) metal coordination : bond 0.02389 ( 16) metal coordination : angle 6.41855 ( 18) covalent geometry : bond 0.00365 (15420) covalent geometry : angle 0.71687 (22096) *********************** 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 480 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 442 time to evaluate : 1.358 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: 0.8406 (m-80) cc_final: 0.8032 (m-80) REVERT: A 93 GLN cc_start: 0.8094 (tp40) cc_final: 0.7345 (tp40) REVERT: A 94 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8707 (mm-30) REVERT: A 120 MET cc_start: 0.8512 (mmm) cc_final: 0.8071 (mtp) REVERT: A 129 ARG cc_start: 0.8920 (tpm170) cc_final: 0.8499 (tpm170) REVERT: B 24 ASP cc_start: 0.8045 (t0) cc_final: 0.7770 (t0) REVERT: B 49 LEU cc_start: 0.8873 (mm) cc_final: 0.8513 (tp) REVERT: B 61 PHE cc_start: 0.9150 (t80) cc_final: 0.8932 (t80) REVERT: B 79 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8544 (ptpp) REVERT: B 88 TYR cc_start: 0.9184 (m-10) cc_final: 0.8859 (m-80) REVERT: C 38 ASN cc_start: 0.8759 (m-40) cc_final: 0.8397 (p0) REVERT: C 39 TYR cc_start: 0.9277 (m-80) cc_final: 0.8959 (m-80) REVERT: C 56 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.8996 (mt-10) REVERT: C 64 GLU cc_start: 0.9293 (tm-30) cc_final: 0.9090 (tm-30) REVERT: C 68 ASN cc_start: 0.9363 (m-40) cc_final: 0.8949 (m110) REVERT: C 75 LYS cc_start: 0.8649 (mmmm) cc_final: 0.8219 (mmmm) REVERT: C 95 LYS cc_start: 0.9350 (tttp) cc_final: 0.9098 (tptp) REVERT: C 101 THR cc_start: 0.8851 (m) cc_final: 0.8365 (p) REVERT: C 104 GLN cc_start: 0.8313 (mp10) cc_final: 0.8036 (mp-120) REVERT: D 33 ARG cc_start: 0.8722 (tpt170) cc_final: 0.8003 (mmt90) REVERT: D 47 GLN cc_start: 0.9331 (tm-30) cc_final: 0.9001 (tm-30) REVERT: D 80 LEU cc_start: 0.9691 (tp) cc_final: 0.9397 (tp) REVERT: D 96 THR cc_start: 0.9570 (m) cc_final: 0.9290 (p) REVERT: E 50 GLU cc_start: 0.9329 (pt0) cc_final: 0.8651 (pp20) REVERT: E 105 GLU cc_start: 0.8650 (pp20) cc_final: 0.8172 (pp20) REVERT: E 120 MET cc_start: 0.8544 (mmm) cc_final: 0.8120 (mmm) REVERT: E 125 GLN cc_start: 0.9446 (mt0) cc_final: 0.9052 (mp10) REVERT: F 27 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8711 (mp10) REVERT: F 35 ARG cc_start: 0.9279 (ttm-80) cc_final: 0.9027 (ttm-80) REVERT: F 39 ARG cc_start: 0.9045 (mmt90) cc_final: 0.8523 (mmt90) REVERT: F 44 LYS cc_start: 0.9422 (tptm) cc_final: 0.9207 (tppp) REVERT: F 78 ARG cc_start: 0.8416 (ttp80) cc_final: 0.8069 (ttp80) REVERT: F 79 LYS cc_start: 0.8850 (mtpp) cc_final: 0.8573 (mtmm) REVERT: F 88 TYR cc_start: 0.9368 (m-10) cc_final: 0.8853 (m-10) REVERT: G 32 ARG cc_start: 0.9372 (ttp80) cc_final: 0.8756 (ttp80) REVERT: G 36 LYS cc_start: 0.9214 (mmtm) cc_final: 0.8742 (mmtm) REVERT: G 38 ASN cc_start: 0.9113 (m-40) cc_final: 0.8817 (t0) REVERT: G 39 TYR cc_start: 0.9174 (m-80) cc_final: 0.8914 (m-80) REVERT: G 42 ARG cc_start: 0.8740 (ptp-110) cc_final: 0.8107 (ptm-80) REVERT: G 57 TYR cc_start: 0.9250 (t80) cc_final: 0.8411 (t80) REVERT: G 61 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8294 (mp0) REVERT: G 81 ARG cc_start: 0.9151 (tpt170) cc_final: 0.8899 (tpt170) REVERT: H 33 ARG cc_start: 0.8562 (tpp80) cc_final: 0.8157 (tpp80) REVERT: H 40 TYR cc_start: 0.9286 (m-80) cc_final: 0.8849 (m-80) REVERT: H 47 GLN cc_start: 0.8980 (tm-30) cc_final: 0.8664 (tm-30) REVERT: H 68 ASP cc_start: 0.9230 (t0) cc_final: 0.8898 (t0) REVERT: H 72 ARG cc_start: 0.9343 (ttm170) cc_final: 0.9070 (ptm160) REVERT: H 83 TYR cc_start: 0.8735 (m-10) cc_final: 0.8233 (m-80) REVERT: H 84 ASN cc_start: 0.8980 (m110) cc_final: 0.8649 (m-40) REVERT: H 86 ARG cc_start: 0.9319 (tpp80) cc_final: 0.8871 (tpp80) REVERT: H 95 GLN cc_start: 0.9560 (pt0) cc_final: 0.9271 (tt0) REVERT: H 96 THR cc_start: 0.9608 (m) cc_final: 0.9342 (p) REVERT: K 51 LEU cc_start: 0.9461 (tt) cc_final: 0.9066 (tp) REVERT: K 54 GLN cc_start: 0.9277 (pp30) cc_final: 0.9041 (pp30) REVERT: N 29 ASP cc_start: 0.6738 (t70) cc_final: 0.6214 (p0) REVERT: N 38 MET cc_start: 0.4278 (ppp) cc_final: 0.3886 (ppp) REVERT: N 136 ARG cc_start: 0.9238 (mmp80) cc_final: 0.9003 (mmp80) REVERT: N 140 GLU cc_start: 0.9204 (pt0) cc_final: 0.8959 (pt0) outliers start: 38 outliers final: 25 residues processed: 455 average time/residue: 0.3269 time to fit residues: 201.8909 Evaluate side-chains 435 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 408 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 47 SER 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 79 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain N residue 37 ILE 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 37 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 113 optimal weight: 0.3980 chunk 97 optimal weight: 7.9990 chunk 40 optimal weight: 0.1980 chunk 9 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- 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** ** B 27 GLN ** 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** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.051739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.041156 restraints weight = 94874.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.042365 restraints weight = 45424.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.043201 restraints weight = 27952.306| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 15436 Z= 0.204 Angle : 0.787 15.022 22114 Z= 0.414 Chirality : 0.041 0.335 2519 Planarity : 0.005 0.072 1788 Dihedral : 29.597 172.954 4403 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.76 % Rotamer: Outliers : 3.94 % Allowed : 34.50 % Favored : 61.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1062 helix: 1.11 (0.20), residues: 677 sheet: 1.16 (1.29), residues: 24 loop : -0.73 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP N 93 HIS 0.004 0.001 HIS K 41 PHE 0.037 0.002 PHE E 67 TYR 0.022 0.002 TYR D 40 ARG 0.013 0.001 ARG H 79 Details of bonding type rmsd hydrogen bonds : bond 0.04589 ( 872) hydrogen bonds : angle 3.61993 ( 2220) metal coordination : bond 0.02357 ( 16) metal coordination : angle 6.70234 ( 18) covalent geometry : bond 0.00466 (15420) covalent geometry : angle 0.76347 (22096) *********************** 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 455 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 419 time to evaluate : 1.150 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: 0.8381 (m-80) cc_final: 0.8030 (m-80) REVERT: A 120 MET cc_start: 0.8571 (mmm) cc_final: 0.8152 (mtt) REVERT: A 129 ARG cc_start: 0.8942 (tpm170) cc_final: 0.8509 (tpm170) REVERT: B 24 ASP cc_start: 0.7898 (t0) cc_final: 0.7666 (t0) REVERT: B 49 LEU cc_start: 0.8817 (mm) cc_final: 0.8519 (tp) REVERT: B 63 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8446 (pm20) REVERT: B 67 ARG cc_start: 0.8761 (ttm110) cc_final: 0.8443 (ttm110) REVERT: B 79 LYS cc_start: 0.8970 (ptpt) cc_final: 0.8610 (ptpp) REVERT: B 88 TYR cc_start: 0.9225 (m-10) cc_final: 0.8859 (m-80) REVERT: C 38 ASN cc_start: 0.8840 (m-40) cc_final: 0.8522 (p0) REVERT: C 39 TYR cc_start: 0.9284 (m-80) cc_final: 0.9007 (m-80) REVERT: C 64 GLU cc_start: 0.9294 (tm-30) cc_final: 0.8977 (tm-30) REVERT: C 68 ASN cc_start: 0.9329 (m-40) cc_final: 0.8885 (m-40) REVERT: C 75 LYS cc_start: 0.8683 (mmmm) cc_final: 0.8286 (mmmm) REVERT: C 95 LYS cc_start: 0.9362 (tttp) cc_final: 0.9144 (tptp) REVERT: C 101 THR cc_start: 0.8835 (m) cc_final: 0.8389 (p) REVERT: C 104 GLN cc_start: 0.8509 (mp10) cc_final: 0.8173 (mp10) REVERT: D 47 GLN cc_start: 0.9377 (tm-30) cc_final: 0.9040 (tm-30) REVERT: D 68 ASP cc_start: 0.9464 (t0) cc_final: 0.9075 (t0) REVERT: D 80 LEU cc_start: 0.9689 (tp) cc_final: 0.9420 (tp) REVERT: D 93 GLU cc_start: 0.9095 (pm20) cc_final: 0.8834 (pm20) REVERT: D 96 THR cc_start: 0.9587 (m) cc_final: 0.9291 (p) REVERT: D 105 GLU cc_start: 0.8089 (pm20) cc_final: 0.7676 (pm20) REVERT: D 108 LYS cc_start: 0.9466 (ptmt) cc_final: 0.9126 (pttp) REVERT: E 105 GLU cc_start: 0.8618 (pp20) cc_final: 0.8076 (pp20) REVERT: E 120 MET cc_start: 0.8611 (mmm) cc_final: 0.8137 (mmm) REVERT: E 125 GLN cc_start: 0.9435 (mt0) cc_final: 0.9065 (mp10) REVERT: E 133 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8573 (mp0) REVERT: F 35 ARG cc_start: 0.9332 (ttm-80) cc_final: 0.9016 (ttm-80) REVERT: F 44 LYS cc_start: 0.9459 (tptm) cc_final: 0.8898 (mmmt) REVERT: F 78 ARG cc_start: 0.8516 (ttp80) cc_final: 0.8156 (ttp80) REVERT: F 79 LYS cc_start: 0.8939 (mtpp) cc_final: 0.8547 (mtmm) REVERT: F 88 TYR cc_start: 0.9349 (m-10) cc_final: 0.9067 (m-80) REVERT: F 93 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8472 (mp10) REVERT: G 32 ARG cc_start: 0.9378 (ttp80) cc_final: 0.8698 (ttp80) REVERT: G 36 LYS cc_start: 0.9240 (mmtm) cc_final: 0.8845 (mmtm) REVERT: G 38 ASN cc_start: 0.9199 (m-40) cc_final: 0.8971 (t0) REVERT: G 42 ARG cc_start: 0.8769 (ptp-110) cc_final: 0.8059 (ptm-80) REVERT: G 75 LYS cc_start: 0.9295 (mmtt) cc_final: 0.8582 (mmmm) REVERT: G 81 ARG cc_start: 0.9200 (tpt170) cc_final: 0.8901 (tpt170) REVERT: G 90 ASP cc_start: 0.8552 (t0) cc_final: 0.8017 (t0) REVERT: H 33 ARG cc_start: 0.8645 (tpp80) cc_final: 0.8334 (tpp80) REVERT: H 35 GLU cc_start: 0.8168 (tp30) cc_final: 0.7896 (tp30) REVERT: H 68 ASP cc_start: 0.9238 (t0) cc_final: 0.8868 (t0) REVERT: H 72 ARG cc_start: 0.9292 (ttm170) cc_final: 0.8996 (ptm160) REVERT: H 84 ASN cc_start: 0.8921 (m110) cc_final: 0.8595 (m-40) REVERT: H 86 ARG cc_start: 0.9323 (tpp80) cc_final: 0.9118 (tpp80) REVERT: H 92 ARG cc_start: 0.8909 (mtp-110) cc_final: 0.8384 (ttp80) REVERT: M 104 MET cc_start: 0.8853 (mmm) cc_final: 0.8550 (mmm) REVERT: N 38 MET cc_start: 0.4265 (ppp) cc_final: 0.3887 (ppp) REVERT: N 140 GLU cc_start: 0.9129 (pt0) cc_final: 0.8892 (pt0) outliers start: 36 outliers final: 25 residues processed: 432 average time/residue: 0.3517 time to fit residues: 204.9857 Evaluate side-chains 437 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 410 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER 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 34 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 ILE 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 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 112 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain N residue 37 ILE 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 53 optimal weight: 0.0980 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 17 optimal weight: 0.0060 chunk 125 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 118 optimal weight: 0.0020 overall best weight: 0.4206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN E 93 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.053838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.043301 restraints weight = 92210.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.044561 restraints weight = 43493.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.045417 restraints weight = 26262.316| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4164 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= 0.167 Angle : 0.801 14.159 22114 Z= 0.420 Chirality : 0.041 0.400 2519 Planarity : 0.005 0.068 1788 Dihedral : 29.500 173.220 4403 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.76 % Rotamer: Outliers : 3.18 % Allowed : 34.94 % Favored : 61.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.26), residues: 1062 helix: 1.06 (0.20), residues: 665 sheet: 1.49 (1.28), residues: 23 loop : -0.87 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 93 HIS 0.004 0.001 HIS K 41 PHE 0.032 0.002 PHE E 67 TYR 0.036 0.002 TYR H 83 ARG 0.009 0.001 ARG N 136 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 872) hydrogen bonds : angle 3.57863 ( 2220) metal coordination : bond 0.02290 ( 16) metal coordination : angle 6.01844 ( 18) covalent geometry : bond 0.00370 (15420) covalent geometry : angle 0.78314 (22096) *********************** 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 468 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 439 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.8341 (m-80) cc_final: 0.7996 (m-80) REVERT: A 94 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8861 (mm-30) REVERT: A 120 MET cc_start: 0.8479 (mmm) cc_final: 0.7976 (mtp) REVERT: A 129 ARG cc_start: 0.8980 (tpm170) cc_final: 0.8523 (tpm170) REVERT: B 24 ASP cc_start: 0.8039 (t0) cc_final: 0.7761 (t0) REVERT: B 49 LEU cc_start: 0.8757 (mm) cc_final: 0.8533 (tp) REVERT: B 52 GLU cc_start: 0.8326 (pm20) cc_final: 0.8122 (pm20) REVERT: B 53 GLU cc_start: 0.7793 (pm20) cc_final: 0.7520 (pm20) REVERT: B 67 ARG cc_start: 0.8718 (ttm110) cc_final: 0.8382 (ttm110) REVERT: B 79 LYS cc_start: 0.8938 (ptpt) cc_final: 0.8606 (ptpp) REVERT: B 88 TYR cc_start: 0.9156 (m-10) cc_final: 0.8854 (m-80) REVERT: C 38 ASN cc_start: 0.8785 (m-40) cc_final: 0.8454 (p0) REVERT: C 64 GLU cc_start: 0.9269 (tm-30) cc_final: 0.9014 (tm-30) REVERT: C 68 ASN cc_start: 0.9346 (m-40) cc_final: 0.8920 (m110) REVERT: C 75 LYS cc_start: 0.8599 (mmmm) cc_final: 0.8151 (mmmm) REVERT: C 84 GLN cc_start: 0.9463 (tp-100) cc_final: 0.9263 (tp-100) REVERT: C 95 LYS cc_start: 0.9349 (tttp) cc_final: 0.9122 (tptp) REVERT: C 101 THR cc_start: 0.8785 (m) cc_final: 0.8342 (p) REVERT: C 104 GLN cc_start: 0.8480 (mp10) cc_final: 0.8136 (mp-120) REVERT: D 47 GLN cc_start: 0.9369 (tm-30) cc_final: 0.9040 (tm-30) REVERT: D 68 ASP cc_start: 0.9503 (t0) cc_final: 0.9278 (t0) REVERT: D 80 LEU cc_start: 0.9681 (tp) cc_final: 0.9402 (tp) REVERT: D 93 GLU cc_start: 0.9030 (pm20) cc_final: 0.8725 (pm20) REVERT: D 96 THR cc_start: 0.9560 (m) cc_final: 0.9275 (p) REVERT: D 105 GLU cc_start: 0.8195 (pm20) cc_final: 0.7877 (pm20) REVERT: D 108 LYS cc_start: 0.9470 (ptmt) cc_final: 0.9090 (pttp) REVERT: D 120 LYS cc_start: 0.9404 (ttpp) cc_final: 0.9115 (ttpp) REVERT: E 105 GLU cc_start: 0.8725 (pp20) cc_final: 0.8207 (pp20) REVERT: E 120 MET cc_start: 0.8536 (mmm) cc_final: 0.8064 (mmm) REVERT: E 125 GLN cc_start: 0.9417 (mt0) cc_final: 0.9023 (mp10) REVERT: E 133 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8610 (mp0) REVERT: F 35 ARG cc_start: 0.9227 (ttm-80) cc_final: 0.8928 (ttm-80) REVERT: F 44 LYS cc_start: 0.9386 (tptm) cc_final: 0.9166 (mmtp) REVERT: F 78 ARG cc_start: 0.8413 (ttp80) cc_final: 0.8112 (ttp80) REVERT: F 79 LYS cc_start: 0.8830 (mtpp) cc_final: 0.8520 (mtmm) REVERT: F 88 TYR cc_start: 0.9145 (m-10) cc_final: 0.8592 (m-80) REVERT: F 93 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8433 (mp10) REVERT: G 32 ARG cc_start: 0.9376 (ttp80) cc_final: 0.8656 (ttp80) REVERT: G 35 ARG cc_start: 0.8875 (mtm110) cc_final: 0.8190 (mtm-85) REVERT: G 36 LYS cc_start: 0.9247 (mmtm) cc_final: 0.8947 (mmtm) REVERT: G 38 ASN cc_start: 0.9091 (m-40) cc_final: 0.8838 (t0) REVERT: G 39 TYR cc_start: 0.9136 (m-80) cc_final: 0.8878 (m-80) REVERT: G 42 ARG cc_start: 0.8757 (ptp-110) cc_final: 0.8079 (ptm-80) REVERT: G 57 TYR cc_start: 0.9154 (t80) cc_final: 0.8504 (t80) REVERT: G 61 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8650 (mt-10) REVERT: G 75 LYS cc_start: 0.9233 (mmtt) cc_final: 0.8955 (mmtm) REVERT: G 90 ASP cc_start: 0.8701 (t0) cc_final: 0.8494 (t0) REVERT: H 33 ARG cc_start: 0.8617 (tpp80) cc_final: 0.8354 (tpp80) REVERT: H 40 TYR cc_start: 0.9307 (m-80) cc_final: 0.8872 (m-80) REVERT: H 42 TYR cc_start: 0.8663 (t80) cc_final: 0.8376 (t80) REVERT: H 68 ASP cc_start: 0.9227 (t0) cc_final: 0.8825 (t0) REVERT: H 72 ARG cc_start: 0.9343 (OUTLIER) cc_final: 0.9026 (ptm160) REVERT: H 84 ASN cc_start: 0.8812 (m110) cc_final: 0.8443 (m-40) REVERT: H 86 ARG cc_start: 0.9320 (tpp80) cc_final: 0.8907 (tpp80) REVERT: H 92 ARG cc_start: 0.8939 (mtp-110) cc_final: 0.8355 (ttp80) REVERT: H 93 GLU cc_start: 0.8959 (pm20) cc_final: 0.8451 (pm20) REVERT: N 29 ASP cc_start: 0.6932 (t70) cc_final: 0.6317 (p0) REVERT: N 30 MET cc_start: 0.8208 (tpp) cc_final: 0.7748 (tpp) REVERT: N 38 MET cc_start: 0.4291 (ppp) cc_final: 0.3895 (ppp) REVERT: N 60 TYR cc_start: 0.7336 (t80) cc_final: 0.6972 (t80) REVERT: N 140 GLU cc_start: 0.9128 (pt0) cc_final: 0.8896 (pt0) outliers start: 29 outliers final: 18 residues processed: 450 average time/residue: 0.4673 time to fit residues: 288.2109 Evaluate side-chains 428 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 408 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASN 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 93 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain N residue 37 ILE 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 116 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.053732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.043357 restraints weight = 93410.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.044590 restraints weight = 44350.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.045428 restraints weight = 26890.489| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.214 15436 Z= 0.261 Angle : 0.981 59.189 22114 Z= 0.547 Chirality : 0.047 0.592 2519 Planarity : 0.006 0.068 1788 Dihedral : 29.484 173.217 4403 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.24 % Favored : 95.67 % Rotamer: Outliers : 2.85 % Allowed : 36.14 % Favored : 61.01 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1062 helix: 0.95 (0.19), residues: 671 sheet: 1.48 (1.28), residues: 23 loop : -0.85 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 93 HIS 0.007 0.001 HIS F 75 PHE 0.061 0.003 PHE A 67 TYR 0.037 0.002 TYR H 83 ARG 0.029 0.001 ARG G 29 Details of bonding type rmsd hydrogen bonds : bond 0.04232 ( 872) hydrogen bonds : angle 3.63311 ( 2220) metal coordination : bond 0.02185 ( 16) metal coordination : angle 6.01685 ( 18) covalent geometry : bond 0.00625 (15420) covalent geometry : angle 0.96601 (22096) ********************** 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 435 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 409 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.8314 (m-80) cc_final: 0.7980 (m-80) REVERT: A 94 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8878 (mm-30) REVERT: A 120 MET cc_start: 0.8495 (mmm) cc_final: 0.7999 (mtp) REVERT: A 129 ARG cc_start: 0.8980 (tpm170) cc_final: 0.8524 (tpm170) REVERT: B 67 ARG cc_start: 0.8717 (ttm110) cc_final: 0.8386 (ttm110) REVERT: B 79 LYS cc_start: 0.8973 (ptpt) cc_final: 0.8632 (ptpp) REVERT: B 88 TYR cc_start: 0.9209 (m-10) cc_final: 0.8849 (m-80) REVERT: C 38 ASN cc_start: 0.8810 (m-40) cc_final: 0.8411 (m-40) REVERT: C 64 GLU cc_start: 0.9268 (tm-30) cc_final: 0.9068 (tm-30) REVERT: C 68 ASN cc_start: 0.9343 (m-40) cc_final: 0.8932 (m110) REVERT: C 75 LYS cc_start: 0.8620 (mmmm) cc_final: 0.8214 (mmmm) REVERT: C 84 GLN cc_start: 0.9464 (tp-100) cc_final: 0.9257 (tp-100) REVERT: C 95 LYS cc_start: 0.9348 (tttp) cc_final: 0.9118 (tptp) REVERT: C 101 THR cc_start: 0.8791 (m) cc_final: 0.8344 (p) REVERT: C 104 GLN cc_start: 0.8478 (mp10) cc_final: 0.8132 (mp-120) REVERT: D 47 GLN cc_start: 0.9350 (tm-30) cc_final: 0.9032 (tm-30) REVERT: D 68 ASP cc_start: 0.9504 (t0) cc_final: 0.9282 (t0) REVERT: D 80 LEU cc_start: 0.9683 (tp) cc_final: 0.9415 (tp) REVERT: D 93 GLU cc_start: 0.8977 (pm20) cc_final: 0.8743 (pm20) REVERT: D 96 THR cc_start: 0.9559 (m) cc_final: 0.9282 (p) REVERT: D 105 GLU cc_start: 0.8301 (pm20) cc_final: 0.7839 (pm20) REVERT: D 108 LYS cc_start: 0.9479 (ptmt) cc_final: 0.9100 (pttp) REVERT: D 120 LYS cc_start: 0.9410 (ttpp) cc_final: 0.9119 (ttpp) REVERT: E 105 GLU cc_start: 0.8689 (pp20) cc_final: 0.8167 (pp20) REVERT: E 120 MET cc_start: 0.8533 (mmm) cc_final: 0.8068 (mmm) REVERT: E 125 GLN cc_start: 0.9406 (mt0) cc_final: 0.9025 (mp10) REVERT: E 133 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8620 (mp0) REVERT: F 35 ARG cc_start: 0.9281 (ttm-80) cc_final: 0.9000 (ttm-80) REVERT: F 44 LYS cc_start: 0.9399 (tptm) cc_final: 0.9167 (mmtp) REVERT: F 78 ARG cc_start: 0.8439 (ttp80) cc_final: 0.8117 (ttp80) REVERT: F 79 LYS cc_start: 0.8859 (mtpp) cc_final: 0.8506 (mtmm) REVERT: F 88 TYR cc_start: 0.9035 (m-10) cc_final: 0.8426 (m-80) REVERT: F 93 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8447 (mp10) REVERT: G 32 ARG cc_start: 0.9352 (ttp80) cc_final: 0.8665 (ttp80) REVERT: G 35 ARG cc_start: 0.8872 (mtm110) cc_final: 0.8210 (mtm-85) REVERT: G 36 LYS cc_start: 0.9241 (mmtm) cc_final: 0.8960 (mmtm) REVERT: G 38 ASN cc_start: 0.9082 (m-40) cc_final: 0.8845 (t0) REVERT: G 42 ARG cc_start: 0.8763 (ptp-110) cc_final: 0.8126 (ptm-80) REVERT: G 57 TYR cc_start: 0.9171 (t80) cc_final: 0.8502 (t80) REVERT: G 61 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8642 (mt-10) REVERT: G 75 LYS cc_start: 0.9245 (mmtt) cc_final: 0.8556 (mmmm) REVERT: H 33 ARG cc_start: 0.8621 (tpp80) cc_final: 0.8347 (tpp80) REVERT: H 40 TYR cc_start: 0.9262 (m-80) cc_final: 0.8882 (m-80) REVERT: H 42 TYR cc_start: 0.8675 (t80) cc_final: 0.8381 (t80) REVERT: H 68 ASP cc_start: 0.9206 (t0) cc_final: 0.8825 (t0) REVERT: H 72 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.9030 (ptm160) REVERT: H 84 ASN cc_start: 0.8803 (m110) cc_final: 0.8452 (m-40) REVERT: H 86 ARG cc_start: 0.9325 (tpp80) cc_final: 0.8904 (tpp80) REVERT: H 92 ARG cc_start: 0.8936 (mtp-110) cc_final: 0.8423 (ttp80) REVERT: N 30 MET cc_start: 0.8193 (tpp) cc_final: 0.7581 (tpp) REVERT: N 38 MET cc_start: 0.4287 (ppp) cc_final: 0.3890 (ppp) REVERT: N 60 TYR cc_start: 0.7315 (t80) cc_final: 0.6968 (t80) REVERT: N 140 GLU cc_start: 0.9130 (pt0) cc_final: 0.8893 (pt0) outliers start: 26 outliers final: 22 residues processed: 420 average time/residue: 0.3304 time to fit residues: 189.3677 Evaluate side-chains 432 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 408 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER 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 93 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 50 LYS Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain N residue 37 ILE 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 66 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 40 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 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 = 0.3244 r_free = 0.3244 target = 0.053765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.043356 restraints weight = 93944.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.044579 restraints weight = 44488.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.045449 restraints weight = 27249.251| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.006 0.214 15436 Z= 0.261 Angle : 0.981 59.189 22114 Z= 0.547 Chirality : 0.047 0.592 2519 Planarity : 0.006 0.068 1788 Dihedral : 29.484 173.217 4403 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.24 % Favored : 95.67 % Rotamer: Outliers : 2.63 % Allowed : 36.58 % Favored : 60.79 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1062 helix: 0.95 (0.19), residues: 671 sheet: 1.48 (1.28), residues: 23 loop : -0.85 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 93 HIS 0.007 0.001 HIS F 75 PHE 0.061 0.003 PHE A 67 TYR 0.037 0.002 TYR H 83 ARG 0.029 0.001 ARG G 29 Details of bonding type rmsd hydrogen bonds : bond 0.04232 ( 872) hydrogen bonds : angle 3.63311 ( 2220) metal coordination : bond 0.02185 ( 16) metal coordination : angle 6.01685 ( 18) covalent geometry : bond 0.00625 (15420) covalent geometry : angle 0.96602 (22096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5692.66 seconds wall clock time: 103 minutes 47.50 seconds (6227.50 seconds total)