Starting phenix.real_space_refine on Tue Nov 14 02:03:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3f_13179/11_2023/7p3f_13179_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3f_13179/11_2023/7p3f_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_13179/11_2023/7p3f_13179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3f_13179/11_2023/7p3f_13179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3f_13179/11_2023/7p3f_13179_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3f_13179/11_2023/7p3f_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-1.21rc1-5144/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: 4.55, per 1000 atoms: 0.66 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: 3.48 Conformation dependent library (CDL) restraints added in 877.0 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: 3.62 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: 2.14 Time building geometry restraints manager: 3.60 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: 3228 28.18 - 56.36: 564 56.36 - 84.53: 95 84.53 - 112.71: 5 112.71 - 140.89: 2 Dihedral angle restraints: 3894 sinusoidal: 2190 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 3891 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: 3.480 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: 0.010 Extract box with map and model: 9.600 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 26.850 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.450 ------------------------------------------------------------------------------- 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 : 25.230 140.891 2782 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 *********************** 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 : 0.573 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 132 average time/residue: 0.2871 time to fit residues: 46.8381 Evaluate side-chains 110 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.778 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 38 optimal weight: 0.0010 chunk 59 optimal weight: 10.0000 overall best weight: 0.8988 ------------------------------------------------------------------------------- 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: 0.7737 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7202 Z= 0.210 Angle : 0.577 7.044 10226 Z= 0.338 Chirality : 0.037 0.129 1156 Planarity : 0.005 0.043 940 Dihedral : 28.784 138.363 1682 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.99 % Allowed : 13.29 % Favored : 85.71 % 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: -0.89 (0.35), residues: 580 helix: 0.36 (0.33), residues: 266 sheet: -1.48 (0.46), residues: 114 loop : -1.15 (0.44), residues: 200 *********************** 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 104 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 0.644 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 103 average time/residue: 0.2850 time to fit residues: 35.8240 Evaluate side-chains 96 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.575 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0604 time to fit residues: 1.1804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 0.4980 chunk 18 optimal weight: 0.0010 chunk 49 optimal weight: 0.0050 chunk 40 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7202 Z= 0.151 Angle : 0.506 4.821 10226 Z= 0.297 Chirality : 0.034 0.180 1156 Planarity : 0.004 0.041 940 Dihedral : 28.389 147.070 1682 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.19 % Allowed : 14.09 % Favored : 84.72 % 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: -0.26 (0.36), residues: 580 helix: 0.79 (0.34), residues: 270 sheet: -1.07 (0.47), residues: 114 loop : -0.78 (0.45), residues: 196 *********************** 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 118 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 0.598 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 115 average time/residue: 0.2504 time to fit residues: 35.6324 Evaluate side-chains 103 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 0.554 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0654 time to fit residues: 1.1680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.7738 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7202 Z= 0.194 Angle : 0.507 5.245 10226 Z= 0.296 Chirality : 0.034 0.137 1156 Planarity : 0.004 0.042 940 Dihedral : 28.168 142.906 1682 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.79 % Allowed : 15.28 % Favored : 82.94 % 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: -0.09 (0.37), residues: 580 helix: 0.82 (0.34), residues: 270 sheet: -0.74 (0.49), residues: 114 loop : -0.71 (0.46), residues: 196 *********************** 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 109 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.645 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 105 average time/residue: 0.2656 time to fit residues: 34.4628 Evaluate side-chains 106 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.629 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0613 time to fit residues: 1.7063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 0.0070 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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: 0.7715 moved from start: 0.3458 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= 0.173 Angle : 0.483 5.402 10226 Z= 0.283 Chirality : 0.033 0.126 1156 Planarity : 0.004 0.041 940 Dihedral : 28.104 145.077 1682 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.99 % Allowed : 14.88 % Favored : 84.13 % 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: -0.03 (0.36), residues: 580 helix: 0.83 (0.34), residues: 266 sheet: -0.59 (0.49), residues: 116 loop : -0.66 (0.45), residues: 198 *********************** 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 110 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 0.570 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 108 average time/residue: 0.2619 time to fit residues: 35.0200 Evaluate side-chains 101 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 0.641 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0766 time to fit residues: 1.2297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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: 0.7818 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7202 Z= 0.334 Angle : 0.553 5.846 10226 Z= 0.316 Chirality : 0.036 0.148 1156 Planarity : 0.005 0.043 940 Dihedral : 28.382 144.799 1682 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % 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: -0.49 (0.36), residues: 580 helix: 0.18 (0.33), residues: 272 sheet: -0.63 (0.50), residues: 114 loop : -0.61 (0.46), residues: 194 *********************** 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 113 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 0.694 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 108 average time/residue: 0.2752 time to fit residues: 36.5224 Evaluate side-chains 107 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 0.672 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0705 time to fit residues: 1.9919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.0770 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 39 optimal weight: 0.2980 chunk 38 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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: 0.7705 moved from start: 0.3797 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= 0.150 Angle : 0.483 6.742 10226 Z= 0.282 Chirality : 0.033 0.129 1156 Planarity : 0.004 0.040 940 Dihedral : 28.118 144.217 1682 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.60 % Allowed : 16.07 % Favored : 83.33 % 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: -0.03 (0.37), residues: 580 helix: 0.70 (0.34), residues: 266 sheet: -0.43 (0.50), residues: 116 loop : -0.55 (0.45), residues: 198 *********************** 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 116 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 113 time to evaluate : 0.639 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 115 average time/residue: 0.2677 time to fit residues: 38.0139 Evaluate side-chains 107 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 0.633 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0730 time to fit residues: 1.0262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0050 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 55 optimal weight: 0.2980 chunk 59 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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: 0.7717 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7202 Z= 0.161 Angle : 0.483 6.502 10226 Z= 0.280 Chirality : 0.033 0.153 1156 Planarity : 0.004 0.040 940 Dihedral : 28.021 144.222 1682 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.40 % Allowed : 19.05 % 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: 0.12 (0.37), residues: 580 helix: 0.74 (0.34), residues: 270 sheet: -0.29 (0.50), residues: 116 loop : -0.41 (0.46), residues: 194 *********************** 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 111 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 109 average time/residue: 0.2795 time to fit residues: 37.5017 Evaluate side-chains 102 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.582 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0617 time to fit residues: 0.9266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 29 optimal weight: 0.4980 chunk 43 optimal weight: 0.2980 chunk 65 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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: 0.7768 moved from start: 0.3876 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= 0.242 Angle : 0.518 6.219 10226 Z= 0.296 Chirality : 0.034 0.145 1156 Planarity : 0.004 0.041 940 Dihedral : 28.030 144.117 1682 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.40 % Allowed : 20.04 % 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: -0.07 (0.36), residues: 580 helix: 0.50 (0.34), residues: 272 sheet: -0.37 (0.49), residues: 116 loop : -0.38 (0.46), residues: 192 *********************** 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 105 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.616 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 104 average time/residue: 0.2885 time to fit residues: 36.7262 Evaluate side-chains 100 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.637 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0626 time to fit residues: 0.9231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 0.0040 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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 30 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4054 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= 0.174 Angle : 0.495 7.831 10226 Z= 0.284 Chirality : 0.033 0.136 1156 Planarity : 0.004 0.040 940 Dihedral : 27.833 143.598 1682 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.20 % Allowed : 20.04 % Favored : 79.76 % 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: 0.10 (0.36), residues: 580 helix: 0.67 (0.34), residues: 270 sheet: -0.31 (0.49), residues: 116 loop : -0.32 (0.46), residues: 194 ********************** 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 101 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 0.650 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 101 average time/residue: 0.2992 time to fit residues: 36.7954 Evaluate side-chains 99 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.590 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 53 optimal weight: 0.0170 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.0060 chunk 46 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 37 optimal weight: 0.1980 chunk 60 optimal weight: 10.0000 chunk 35 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 overall best weight: 0.2434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.202033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.138323 restraints weight = 8160.351| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.70 r_work: 0.3355 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7202 Z= 0.136 Angle : 0.466 6.164 10226 Z= 0.270 Chirality : 0.032 0.129 1156 Planarity : 0.003 0.040 940 Dihedral : 27.661 143.474 1682 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 19.84 % Favored : 80.16 % 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 (0.37), residues: 580 helix: 0.72 (0.35), residues: 266 sheet: -0.18 (0.48), residues: 116 loop : -0.05 (0.47), residues: 198 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1900.87 seconds wall clock time: 34 minutes 57.30 seconds (2097.30 seconds total)