Starting phenix.real_space_refine on Tue Feb 13 16:27:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3f_13179/02_2024/7p3f_13179_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3f_13179/02_2024/7p3f_13179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3f_13179/02_2024/7p3f_13179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3f_13179/02_2024/7p3f_13179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3f_13179/02_2024/7p3f_13179_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3f_13179/02_2024/7p3f_13179_neut_updated.pdb" } resolution = 3.31 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= -0.002 sd= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 124 5.49 5 S 32 5.16 5 C 3858 2.51 5 N 1280 2.21 5 O 1580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 26": "NH1" <-> "NH2" Residue "A ARG 27": "NH1" <-> "NH2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "C ARG 26": "NH1" <-> "NH2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C GLU 138": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6878 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1145 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "C" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1145 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "B" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1145 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "D" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1145 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "F" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1028 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "R" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1022 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {' ZN': 1, 'ATP': 1, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {' ZN': 1, 'ATP': 1, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {' ZN': 1, 'ATP': 1, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {' ZN': 1, 'ATP': 1, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24 SG CYS A 3 103.479 45.542 34.915 1.00 72.57 S ATOM 48 SG CYS A 6 106.815 43.750 34.928 1.00 73.80 S ATOM 254 SG CYS A 31 106.328 46.744 32.620 1.00 72.42 S ATOM 275 SG CYS A 34 104.522 43.517 31.897 1.00 75.24 S ATOM 1169 SG CYS C 3 25.212 44.211 34.884 1.00 72.57 S ATOM 1193 SG CYS C 6 21.877 46.005 34.889 1.00 73.80 S ATOM 1399 SG CYS C 31 22.365 43.005 32.589 1.00 72.42 S ATOM 1420 SG CYS C 34 24.173 46.229 31.860 1.00 75.24 S ATOM 2314 SG CYS B 3 38.685 14.665 40.459 1.00 71.45 S ATOM 2338 SG CYS B 6 40.204 11.612 38.607 1.00 68.82 S ATOM 2544 SG CYS B 31 36.880 12.614 37.317 1.00 74.44 S ATOM 2565 SG CYS B 34 37.290 11.235 41.007 1.00 77.60 S ATOM 3459 SG CYS D 3 89.996 75.111 40.464 1.00 71.45 S ATOM 3483 SG CYS D 6 88.482 78.166 38.612 1.00 68.82 S ATOM 3689 SG CYS D 31 91.806 77.161 37.325 1.00 74.44 S ATOM 3710 SG CYS D 34 91.394 78.539 41.015 1.00 77.60 S Time building chain proxies: 4.40, per 1000 atoms: 0.64 Number of scatterers: 6878 At special positions: 0 Unit cell: (129.31, 90.45, 75.71, 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 32 16.00 P 124 15.00 O 1580 8.00 N 1280 7.00 C 3858 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 - 3.50 Amino acid : False - 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: 3.33 Conformation dependent library (CDL) restraints added in 973.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 203 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 34 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 6 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 3 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 31 " pdb=" ZN B 203 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 6 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 34 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 3 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 31 " pdb=" ZN C 203 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 6 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 3 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 31 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 34 " pdb=" ZN D 203 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 6 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 31 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 34 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 3 " Number of angles added : 24 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1112 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 8 sheets defined 45.2% alpha, 15.0% beta 41 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 60 through 68 removed outlier: 3.522A pdb=" N ASN A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 94 Processing helix chain 'A' and resid 102 through 116 removed outlier: 4.052A pdb=" N GLY A 106 " --> pdb=" O HIS A 103 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A 107 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 110 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY A 111 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Proline residue: A 112 - end of helix Processing helix chain 'A' and resid 118 through 128 removed outlier: 3.936A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 146 Processing helix chain 'C' and resid 60 through 68 removed outlier: 3.522A pdb=" N ASN C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY C 66 " --> pdb=" O LYS C 62 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 94 Processing helix chain 'C' and resid 102 through 116 removed outlier: 4.053A pdb=" N GLY C 106 " --> pdb=" O HIS C 103 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU C 107 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 110 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY C 111 " --> pdb=" O ALA C 108 " (cutoff:3.500A) Proline residue: C 112 - end of helix Processing helix chain 'C' and resid 118 through 128 removed outlier: 3.936A pdb=" N LEU C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 127 " --> pdb=" O ARG C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 146 Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.514A pdb=" N ALA B 70 " --> pdb=" O GLY B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 95 removed outlier: 3.917A pdb=" N THR B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 116 removed outlier: 3.756A pdb=" N GLY B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Proline residue: B 112 - end of helix removed outlier: 3.737A pdb=" N GLU B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 removed outlier: 4.052A pdb=" N VAL B 127 " --> pdb=" O ARG B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 146 removed outlier: 3.597A pdb=" N GLU B 138 " --> pdb=" O GLU B 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.514A pdb=" N ALA D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 95 removed outlier: 3.917A pdb=" N THR D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.756A pdb=" N GLY D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Proline residue: D 112 - end of helix removed outlier: 3.737A pdb=" N GLU D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 128 removed outlier: 4.052A pdb=" N VAL D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 146 removed outlier: 3.597A pdb=" N GLU D 138 " --> pdb=" O GLU D 135 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 37 through 43 removed outlier: 6.326A pdb=" N GLN A 30 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL A 13 " --> pdb=" O GLN A 30 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 55 through 57 Processing sheet with id= C, first strand: chain 'C' and resid 37 through 43 removed outlier: 6.326A pdb=" N GLN C 30 " --> pdb=" O VAL C 13 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL C 13 " --> pdb=" O GLN C 30 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 55 through 57 Processing sheet with id= E, first strand: chain 'B' and resid 37 through 42 removed outlier: 5.612A pdb=" N GLN B 30 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL B 13 " --> pdb=" O GLN B 30 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 55 through 57 Processing sheet with id= G, first strand: chain 'D' and resid 37 through 42 removed outlier: 5.613A pdb=" N GLN D 30 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL D 13 " --> pdb=" O GLN D 30 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 55 through 57 204 hydrogen bonds defined for protein. 522 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 202 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 2.12 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 954 1.31 - 1.44: 2264 1.44 - 1.56: 3706 1.56 - 1.69: 238 1.69 - 1.81: 40 Bond restraints: 7202 Sorted by residual: bond pdb=" CA SER A 133 " pdb=" CB SER A 133 " ideal model delta sigma weight residual 1.532 1.455 0.077 1.56e-02 4.11e+03 2.44e+01 bond pdb=" CA SER C 133 " pdb=" CB SER C 133 " ideal model delta sigma weight residual 1.532 1.455 0.077 1.56e-02 4.11e+03 2.42e+01 bond pdb=" CA ALA A 140 " pdb=" CB ALA A 140 " ideal model delta sigma weight residual 1.528 1.458 0.070 1.56e-02 4.11e+03 2.03e+01 bond pdb=" CA ALA C 140 " pdb=" CB ALA C 140 " ideal model delta sigma weight residual 1.528 1.459 0.070 1.56e-02 4.11e+03 2.00e+01 bond pdb=" C PHE A 131 " pdb=" O PHE A 131 " ideal model delta sigma weight residual 1.235 1.185 0.050 1.15e-02 7.56e+03 1.87e+01 ... (remaining 7197 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.42: 886 106.42 - 113.44: 3788 113.44 - 120.47: 3108 120.47 - 127.50: 2210 127.50 - 134.53: 234 Bond angle restraints: 10226 Sorted by residual: angle pdb=" PB ATP B 201 " pdb=" O3B ATP B 201 " pdb=" PG ATP B 201 " ideal model delta sigma weight residual 139.87 131.73 8.14 1.00e+00 1.00e+00 6.62e+01 angle pdb=" PB ATP D 201 " pdb=" O3B ATP D 201 " pdb=" PG ATP D 201 " ideal model delta sigma weight residual 139.87 131.75 8.12 1.00e+00 1.00e+00 6.60e+01 angle pdb=" PB DTP B 202 " pdb=" O3B DTP B 202 " pdb=" PG DTP B 202 " ideal model delta sigma weight residual 139.87 131.80 8.07 1.00e+00 1.00e+00 6.52e+01 angle pdb=" PB DTP D 202 " pdb=" O3B DTP D 202 " pdb=" PG DTP D 202 " ideal model delta sigma weight residual 139.87 131.82 8.05 1.00e+00 1.00e+00 6.49e+01 angle pdb=" PB DTP C 202 " pdb=" O3B DTP C 202 " pdb=" PG DTP C 202 " ideal model delta sigma weight residual 139.87 132.55 7.32 1.00e+00 1.00e+00 5.36e+01 ... (remaining 10221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.18: 3414 28.18 - 56.36: 687 56.36 - 84.53: 114 84.53 - 112.71: 5 112.71 - 140.89: 2 Dihedral angle restraints: 4222 sinusoidal: 2518 harmonic: 1704 Sorted by residual: dihedral pdb=" C GLU D 42 " pdb=" N GLU D 42 " pdb=" CA GLU D 42 " pdb=" CB GLU D 42 " ideal model delta harmonic sigma weight residual -122.60 -112.04 -10.56 0 2.50e+00 1.60e-01 1.78e+01 dihedral pdb=" C GLU B 42 " pdb=" N GLU B 42 " pdb=" CA GLU B 42 " pdb=" CB GLU B 42 " ideal model delta harmonic sigma weight residual -122.60 -112.09 -10.51 0 2.50e+00 1.60e-01 1.77e+01 dihedral pdb=" C THR C 19 " pdb=" N THR C 19 " pdb=" CA THR C 19 " pdb=" CB THR C 19 " ideal model delta harmonic sigma weight residual -122.00 -132.37 10.37 0 2.50e+00 1.60e-01 1.72e+01 ... (remaining 4219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 846 0.074 - 0.147: 229 0.147 - 0.220: 62 0.220 - 0.293: 15 0.293 - 0.367: 4 Chirality restraints: 1156 Sorted by residual: chirality pdb=" CA THR C 19 " pdb=" N THR C 19 " pdb=" C THR C 19 " pdb=" CB THR C 19 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA THR A 19 " pdb=" N THR A 19 " pdb=" C THR A 19 " pdb=" CB THR A 19 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CA ILE A 141 " pdb=" N ILE A 141 " pdb=" C ILE A 141 " pdb=" CB ILE A 141 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1153 not shown) Planarity restraints: 940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP D 201 " -0.096 2.00e-02 2.50e+03 4.13e-02 4.69e+01 pdb=" C2 ATP D 201 " 0.014 2.00e-02 2.50e+03 pdb=" C4 ATP D 201 " 0.030 2.00e-02 2.50e+03 pdb=" C5 ATP D 201 " 0.024 2.00e-02 2.50e+03 pdb=" C6 ATP D 201 " -0.005 2.00e-02 2.50e+03 pdb=" C8 ATP D 201 " 0.029 2.00e-02 2.50e+03 pdb=" N1 ATP D 201 " -0.004 2.00e-02 2.50e+03 pdb=" N3 ATP D 201 " 0.030 2.00e-02 2.50e+03 pdb=" N6 ATP D 201 " -0.070 2.00e-02 2.50e+03 pdb=" N7 ATP D 201 " 0.031 2.00e-02 2.50e+03 pdb=" N9 ATP D 201 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP B 201 " 0.096 2.00e-02 2.50e+03 4.12e-02 4.66e+01 pdb=" C2 ATP B 201 " -0.014 2.00e-02 2.50e+03 pdb=" C4 ATP B 201 " -0.030 2.00e-02 2.50e+03 pdb=" C5 ATP B 201 " -0.024 2.00e-02 2.50e+03 pdb=" C6 ATP B 201 " 0.005 2.00e-02 2.50e+03 pdb=" C8 ATP B 201 " -0.029 2.00e-02 2.50e+03 pdb=" N1 ATP B 201 " 0.005 2.00e-02 2.50e+03 pdb=" N3 ATP B 201 " -0.030 2.00e-02 2.50e+03 pdb=" N6 ATP B 201 " 0.069 2.00e-02 2.50e+03 pdb=" N7 ATP B 201 " -0.030 2.00e-02 2.50e+03 pdb=" N9 ATP B 201 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 21 " -0.025 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C ASP D 21 " 0.084 2.00e-02 2.50e+03 pdb=" O ASP D 21 " -0.031 2.00e-02 2.50e+03 pdb=" N GLY D 22 " -0.028 2.00e-02 2.50e+03 ... (remaining 937 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1223 2.77 - 3.31: 5915 3.31 - 3.84: 12080 3.84 - 4.37: 15264 4.37 - 4.90: 22233 Nonbonded interactions: 56715 Sorted by model distance: nonbonded pdb=" OG1 THR A 101 " pdb=" OD2 ASP A 104 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR C 101 " pdb=" OD2 ASP C 104 " model vdw 2.242 2.440 nonbonded pdb=" NH1 ARG B 68 " pdb=" OE2 GLU B 78 " model vdw 2.286 2.520 nonbonded pdb=" NH1 ARG D 68 " pdb=" OE2 GLU D 78 " model vdw 2.286 2.520 nonbonded pdb=" O ALA B 70 " pdb=" NH1 ARG B 123 " model vdw 2.420 2.520 ... (remaining 56710 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.080 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 26.350 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 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 : 0.009 0.077 7202 Z= 0.573 Angle : 1.318 10.312 10226 Z= 0.926 Chirality : 0.077 0.367 1156 Planarity : 0.008 0.049 940 Dihedral : 25.952 140.891 3110 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.59 % Allowed : 5.95 % Favored : 92.46 % Cbeta Deviations : 1.08 % Peptide Plane: Cis-proline : 0.00 % 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: -1.22 (0.35), residues: 580 helix: -0.04 (0.31), residues: 270 sheet: -1.47 (0.55), residues: 96 loop : -1.31 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.003 HIS B 103 PHE 0.043 0.004 PHE B 38 TYR 0.011 0.002 TYR B 121 ARG 0.008 0.001 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 0.635 Fit side-chains REVERT: A 17 ARG cc_start: 0.7761 (mmt180) cc_final: 0.7557 (ttp-110) REVERT: A 25 ILE cc_start: 0.8908 (tt) cc_final: 0.8585 (tt) REVERT: A 134 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8141 (pt) REVERT: C 17 ARG cc_start: 0.7739 (mmt180) cc_final: 0.7490 (ttp-110) outliers start: 8 outliers final: 0 residues processed: 132 average time/residue: 0.2558 time to fit residues: 41.5333 Evaluate side-chains 111 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 38 optimal weight: 0.0010 chunk 59 optimal weight: 10.0000 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN D 2 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7202 Z= 0.193 Angle : 0.571 4.456 10226 Z= 0.340 Chirality : 0.037 0.163 1156 Planarity : 0.005 0.044 940 Dihedral : 28.381 139.511 2012 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.60 % Allowed : 13.49 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.77 (0.35), residues: 580 helix: 0.43 (0.33), residues: 266 sheet: -1.34 (0.47), residues: 114 loop : -1.09 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 103 PHE 0.009 0.001 PHE A 124 TYR 0.016 0.002 TYR B 121 ARG 0.003 0.000 ARG A 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 0.879 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 98 average time/residue: 0.2740 time to fit residues: 33.0620 Evaluate side-chains 89 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain C residue 11 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7202 Z= 0.279 Angle : 0.569 4.767 10226 Z= 0.332 Chirality : 0.037 0.232 1156 Planarity : 0.005 0.044 940 Dihedral : 28.106 144.172 2012 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.38 % Allowed : 15.48 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.81 (0.35), residues: 580 helix: 0.20 (0.32), residues: 270 sheet: -1.23 (0.46), residues: 116 loop : -0.89 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 103 PHE 0.017 0.002 PHE A 124 TYR 0.012 0.002 TYR C 121 ARG 0.006 0.000 ARG D 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8317 (tpt90) cc_final: 0.8047 (tpt90) REVERT: C 42 GLU cc_start: 0.7255 (pt0) cc_final: 0.7014 (pt0) outliers start: 12 outliers final: 10 residues processed: 112 average time/residue: 0.2449 time to fit residues: 34.2501 Evaluate side-chains 107 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 97 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 10.0000 chunk 45 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN B 72 GLN D 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7202 Z= 0.289 Angle : 0.563 4.921 10226 Z= 0.325 Chirality : 0.036 0.202 1156 Planarity : 0.005 0.044 940 Dihedral : 28.050 142.911 2010 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.57 % Allowed : 15.28 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.82 (0.35), residues: 580 helix: 0.17 (0.32), residues: 266 sheet: -1.12 (0.47), residues: 114 loop : -0.94 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 103 PHE 0.015 0.002 PHE C 124 TYR 0.015 0.002 TYR C 128 ARG 0.004 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8371 (tpt90) cc_final: 0.7966 (tpt90) REVERT: C 28 ARG cc_start: 0.8391 (tpt90) cc_final: 0.8142 (tpt90) REVERT: C 42 GLU cc_start: 0.7262 (pt0) cc_final: 0.6979 (pt0) outliers start: 18 outliers final: 16 residues processed: 108 average time/residue: 0.2488 time to fit residues: 33.6682 Evaluate side-chains 111 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 44 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 54 optimal weight: 0.0010 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7202 Z= 0.257 Angle : 0.539 4.900 10226 Z= 0.311 Chirality : 0.035 0.191 1156 Planarity : 0.004 0.042 940 Dihedral : 27.966 144.232 2010 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.96 % Allowed : 14.48 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.58 (0.36), residues: 580 helix: 0.30 (0.33), residues: 266 sheet: -0.96 (0.49), residues: 114 loop : -0.75 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 103 PHE 0.013 0.001 PHE A 124 TYR 0.011 0.002 TYR C 128 ARG 0.003 0.000 ARG D 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 95 time to evaluate : 0.594 Fit side-chains REVERT: A 28 ARG cc_start: 0.8371 (tpt90) cc_final: 0.7970 (tpt90) REVERT: C 28 ARG cc_start: 0.8416 (tpt90) cc_final: 0.8152 (tpt90) outliers start: 25 outliers final: 20 residues processed: 113 average time/residue: 0.2580 time to fit residues: 36.4343 Evaluate side-chains 112 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 54 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 0.0370 chunk 61 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7202 Z= 0.222 Angle : 0.526 5.651 10226 Z= 0.305 Chirality : 0.035 0.179 1156 Planarity : 0.004 0.041 940 Dihedral : 27.777 144.554 2010 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.37 % Allowed : 17.46 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.36), residues: 580 helix: 0.41 (0.34), residues: 264 sheet: -0.87 (0.49), residues: 114 loop : -0.61 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 103 PHE 0.011 0.001 PHE A 124 TYR 0.010 0.002 TYR C 128 ARG 0.003 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.684 Fit side-chains REVERT: C 28 ARG cc_start: 0.8406 (tpt90) cc_final: 0.8082 (tpt90) outliers start: 17 outliers final: 16 residues processed: 110 average time/residue: 0.2696 time to fit residues: 37.4147 Evaluate side-chains 110 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 44 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 35 optimal weight: 0.0020 chunk 63 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN B 72 GLN D 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7202 Z= 0.159 Angle : 0.496 6.480 10226 Z= 0.290 Chirality : 0.033 0.157 1156 Planarity : 0.004 0.040 940 Dihedral : 27.305 145.469 2010 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.98 % Allowed : 17.86 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.27 (0.36), residues: 580 helix: 0.48 (0.34), residues: 264 sheet: -0.76 (0.49), residues: 116 loop : -0.49 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 8 PHE 0.008 0.001 PHE C 58 TYR 0.009 0.001 TYR C 128 ARG 0.003 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.610 Fit side-chains REVERT: C 28 ARG cc_start: 0.8382 (tpt90) cc_final: 0.8026 (tpt90) outliers start: 15 outliers final: 10 residues processed: 108 average time/residue: 0.2323 time to fit residues: 31.5952 Evaluate side-chains 107 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain D residue 44 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7202 Z= 0.233 Angle : 0.525 6.465 10226 Z= 0.302 Chirality : 0.034 0.180 1156 Planarity : 0.004 0.041 940 Dihedral : 27.491 145.409 2010 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.77 % Allowed : 16.67 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.36), residues: 580 helix: 0.23 (0.34), residues: 270 sheet: -0.72 (0.49), residues: 116 loop : -0.35 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 103 PHE 0.012 0.002 PHE A 124 TYR 0.009 0.002 TYR C 128 ARG 0.003 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.621 Fit side-chains REVERT: A 28 ARG cc_start: 0.8345 (tpt90) cc_final: 0.8089 (tpt90) REVERT: C 28 ARG cc_start: 0.8432 (tpt90) cc_final: 0.8068 (tpt90) REVERT: C 115 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.5715 (mp0) outliers start: 19 outliers final: 16 residues processed: 107 average time/residue: 0.2323 time to fit residues: 31.4963 Evaluate side-chains 108 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 44 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 0.2980 chunk 65 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN B 8 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7202 Z= 0.184 Angle : 0.518 9.400 10226 Z= 0.300 Chirality : 0.034 0.204 1156 Planarity : 0.004 0.040 940 Dihedral : 27.221 145.036 2010 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.17 % Allowed : 18.25 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.36), residues: 580 helix: 0.30 (0.34), residues: 266 sheet: -0.63 (0.48), residues: 116 loop : -0.38 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 8 PHE 0.013 0.001 PHE A 137 TYR 0.008 0.001 TYR C 128 ARG 0.002 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 0.617 Fit side-chains REVERT: C 28 ARG cc_start: 0.8400 (tpt90) cc_final: 0.8005 (tpt90) REVERT: C 115 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.5598 (mp0) REVERT: D 30 GLN cc_start: 0.7672 (tt0) cc_final: 0.7390 (tt0) outliers start: 16 outliers final: 15 residues processed: 110 average time/residue: 0.2503 time to fit residues: 34.2403 Evaluate side-chains 107 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 44 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7202 Z= 0.197 Angle : 0.525 7.385 10226 Z= 0.303 Chirality : 0.034 0.169 1156 Planarity : 0.004 0.040 940 Dihedral : 27.151 144.943 2010 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.37 % Allowed : 19.05 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.36), residues: 580 helix: 0.29 (0.34), residues: 266 sheet: -0.60 (0.48), residues: 116 loop : -0.35 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 8 PHE 0.009 0.001 PHE A 38 TYR 0.008 0.001 TYR C 128 ARG 0.007 0.000 ARG A 145 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.618 Fit side-chains REVERT: C 28 ARG cc_start: 0.8414 (tpt90) cc_final: 0.8075 (tpt-90) REVERT: C 115 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.5664 (mp0) REVERT: D 30 GLN cc_start: 0.7650 (tt0) cc_final: 0.7378 (tt0) outliers start: 17 outliers final: 15 residues processed: 101 average time/residue: 0.2459 time to fit residues: 31.0864 Evaluate side-chains 102 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 44 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 0.0370 chunk 53 optimal weight: 0.0770 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.196359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.130115 restraints weight = 8023.226| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.59 r_work: 0.3270 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7202 Z= 0.204 Angle : 0.517 7.471 10226 Z= 0.299 Chirality : 0.034 0.174 1156 Planarity : 0.004 0.040 940 Dihedral : 27.135 144.950 2010 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.37 % Allowed : 19.05 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.36), residues: 580 helix: 0.26 (0.34), residues: 266 sheet: -0.57 (0.48), residues: 116 loop : -0.30 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 8 PHE 0.011 0.001 PHE C 38 TYR 0.008 0.001 TYR C 128 ARG 0.007 0.000 ARG A 145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1839.00 seconds wall clock time: 33 minutes 53.94 seconds (2033.94 seconds total)