Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 20:20:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6p_12739/04_2023/7o6p_12739.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6p_12739/04_2023/7o6p_12739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6p_12739/04_2023/7o6p_12739.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6p_12739/04_2023/7o6p_12739.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6p_12739/04_2023/7o6p_12739.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6p_12739/04_2023/7o6p_12739.pdb" } resolution = 2.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.004 sd= 0.042 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5014 2.51 5 N 1451 2.21 5 O 1759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8276 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2010 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 256, 1913 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 256, 1913 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain breaks: 1 bond proxies already assigned to first conformer: 1837 Chain: "B" Number of atoms: 1980 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 255, 1905 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 255, 1905 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain breaks: 1 bond proxies already assigned to first conformer: 1855 Chain: "C" Number of atoms: 1991 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 1901 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 254, 1901 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain breaks: 1 bond proxies already assigned to first conformer: 1833 Chain: "D" Number of atoms: 2027 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 257, 1919 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 257, 1919 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain breaks: 1 bond proxies already assigned to first conformer: 1831 Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "B" Number of atoms: 71 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Conformer: "A" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Residues with excluded nonbonded symmetry interactions: 43 residue: pdb=" N AARG A 20 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 20 " occ=0.50 residue: pdb=" N ASER A 34 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 34 " occ=0.50 residue: pdb=" N AARG A 40 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 40 " occ=0.50 residue: pdb=" N ALYS A 45 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 45 " occ=0.50 residue: pdb=" N AARG A 84 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 84 " occ=0.50 residue: pdb=" N ALYS A 147 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 147 " occ=0.50 residue: pdb=" N ALYS A 181 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 181 " occ=0.50 residue: pdb=" N AARG A 225 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 225 " occ=0.50 residue: pdb=" N AGLU A 238 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 238 " occ=0.50 residue: pdb=" N AARG A 257 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 257 " occ=0.50 residue: pdb=" N ALEU B 37 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU B 37 " occ=0.50 residue: pdb=" N ALYS B 83 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B 83 " occ=0.50 ... (remaining 31 not shown) Time building chain proxies: 8.23, per 1000 atoms: 0.99 Number of scatterers: 8276 At special positions: 0 Unit cell: (81.536, 93.184, 79.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1759 8.00 N 1451 7.00 C 5014 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: 3.73 Conformation dependent library (CDL) restraints added in 2.4 seconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1914 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 53.9% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 30 through 42 removed outlier: 3.507A pdb=" N ASER A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.558A pdb=" N CYS A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A 64 " --> pdb=" O CYS A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 94 Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 129 through 147 removed outlier: 3.726A pdb=" N ILE A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Proline residue: A 145 - end of helix Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 166 through 188 Processing helix chain 'A' and resid 220 through 231 Processing helix chain 'A' and resid 240 through 253 removed outlier: 3.610A pdb=" N VAL A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 257 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.842A pdb=" N GLN B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 94 Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 129 through 147 removed outlier: 3.727A pdb=" N ILE B 142 " --> pdb=" O HIS B 138 " (cutoff:3.500A) Proline residue: B 145 - end of helix Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 166 through 188 Processing helix chain 'B' and resid 221 through 231 Processing helix chain 'B' and resid 240 through 253 removed outlier: 3.606A pdb=" N VAL B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 257 Processing helix chain 'C' and resid 30 through 42 Processing helix chain 'C' and resid 52 through 64 removed outlier: 3.871A pdb=" N ARG C 58 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS C 60 " --> pdb=" O GLY C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 94 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 129 through 147 removed outlier: 3.730A pdb=" N ILE C 142 " --> pdb=" O HIS C 138 " (cutoff:3.500A) Proline residue: C 145 - end of helix Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'C' and resid 166 through 188 Processing helix chain 'C' and resid 220 through 231 Processing helix chain 'C' and resid 240 through 253 removed outlier: 3.597A pdb=" N VAL C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 257 Processing helix chain 'D' and resid 30 through 42 Processing helix chain 'D' and resid 52 through 64 removed outlier: 3.720A pdb=" N GLY D 64 " --> pdb=" O CYS D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 94 Processing helix chain 'D' and resid 112 through 116 Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 129 through 147 removed outlier: 3.732A pdb=" N ILE D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) Proline residue: D 145 - end of helix Processing helix chain 'D' and resid 156 through 160 Processing helix chain 'D' and resid 166 through 188 Processing helix chain 'D' and resid 220 through 231 Processing helix chain 'D' and resid 240 through 253 removed outlier: 3.619A pdb=" N VAL D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 257 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 73 removed outlier: 6.552A pdb=" N VAL A 21 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL A 100 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 23 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N MET A 99 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE A 154 " --> pdb=" O MET A 99 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASN A 101 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET A 262 " --> pdb=" O VAL A 194 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 69 through 73 removed outlier: 6.537A pdb=" N VAL B 21 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N VAL B 100 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU B 23 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N MET B 99 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE B 154 " --> pdb=" O MET B 99 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ASN B 101 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N MET B 262 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL B 194 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N LEU B 264 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N CYS B 196 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL B 266 " --> pdb=" O CYS B 196 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N SER B 198 " --> pdb=" O VAL B 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 69 through 73 removed outlier: 6.563A pdb=" N VAL C 21 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL C 100 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU C 23 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N MET C 99 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE C 154 " --> pdb=" O MET C 99 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ASN C 101 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N LEU C 264 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N CYS C 196 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL C 266 " --> pdb=" O CYS C 196 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N SER C 198 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 69 through 73 removed outlier: 6.558A pdb=" N VAL D 21 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL D 100 " --> pdb=" O VAL D 21 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU D 23 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N MET D 99 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE D 154 " --> pdb=" O MET D 99 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASN D 101 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N LEU D 264 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N CYS D 196 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL D 266 " --> pdb=" O CYS D 196 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N SER D 198 " --> pdb=" O VAL D 266 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1333 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2778 1.34 - 1.46: 1652 1.46 - 1.58: 3658 1.58 - 1.70: 0 1.70 - 1.81: 80 Bond restraints: 8168 Sorted by residual: bond pdb=" CB ALYS D 189 " pdb=" CG ALYS D 189 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.78e+00 bond pdb=" CA GLN D 52 " pdb=" C GLN D 52 " ideal model delta sigma weight residual 1.532 1.520 0.013 9.60e-03 1.09e+04 1.80e+00 bond pdb=" CG1 ILE D 98 " pdb=" CD1 ILE D 98 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.62e+00 bond pdb=" CG1 ILE B 98 " pdb=" CD1 ILE B 98 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.57e+00 bond pdb=" CG1 ILE A 98 " pdb=" CD1 ILE A 98 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.56e+00 ... (remaining 8163 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.72: 179 106.72 - 113.52: 4619 113.52 - 120.32: 2954 120.32 - 127.13: 3264 127.13 - 133.93: 64 Bond angle restraints: 11080 Sorted by residual: angle pdb=" CA SER B 155 " pdb=" C SER B 155 " pdb=" N SER B 156 " ideal model delta sigma weight residual 117.21 120.45 -3.24 1.42e+00 4.96e-01 5.22e+00 angle pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N SER A 156 " ideal model delta sigma weight residual 117.21 120.45 -3.24 1.42e+00 4.96e-01 5.20e+00 angle pdb=" CA SER C 155 " pdb=" C SER C 155 " pdb=" N SER C 156 " ideal model delta sigma weight residual 117.21 120.43 -3.22 1.42e+00 4.96e-01 5.13e+00 angle pdb=" CA SER B 155 " pdb=" C SER B 155 " pdb=" O SER B 155 " ideal model delta sigma weight residual 120.84 117.86 2.98 1.33e+00 5.65e-01 5.01e+00 angle pdb=" C ALA B 256 " pdb=" N BARG B 257 " pdb=" CA BARG B 257 " ideal model delta sigma weight residual 120.38 123.64 -3.26 1.46e+00 4.69e-01 4.99e+00 ... (remaining 11075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 4535 16.21 - 32.42: 316 32.42 - 48.63: 48 48.63 - 64.84: 12 64.84 - 81.05: 5 Dihedral angle restraints: 4916 sinusoidal: 1901 harmonic: 3015 Sorted by residual: dihedral pdb=" CA PRO A 199 " pdb=" C PRO A 199 " pdb=" N TYR A 200 " pdb=" CA TYR A 200 " ideal model delta harmonic sigma weight residual 180.00 163.59 16.41 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA PRO C 199 " pdb=" C PRO C 199 " pdb=" N TYR C 200 " pdb=" CA TYR C 200 " ideal model delta harmonic sigma weight residual 180.00 163.86 16.14 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA CYS A 60 " pdb=" C CYS A 60 " pdb=" N GLU A 61 " pdb=" CA GLU A 61 " ideal model delta harmonic sigma weight residual 180.00 163.94 16.06 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 4913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 458 0.027 - 0.054: 446 0.054 - 0.081: 244 0.081 - 0.108: 83 0.108 - 0.135: 33 Chirality restraints: 1264 Sorted by residual: chirality pdb=" CB ILE A 192 " pdb=" CA ILE A 192 " pdb=" CG1 ILE A 192 " pdb=" CG2 ILE A 192 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CB ILE C 192 " pdb=" CA ILE C 192 " pdb=" CG1 ILE C 192 " pdb=" CG2 ILE C 192 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CB ILE D 192 " pdb=" CA ILE D 192 " pdb=" CG1 ILE D 192 " pdb=" CG2 ILE D 192 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 1261 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 198 " 0.035 5.00e-02 4.00e+02 5.22e-02 4.37e+00 pdb=" N PRO B 199 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 199 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 199 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 198 " -0.034 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO D 199 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 199 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 199 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 198 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO A 199 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 199 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 199 " 0.027 5.00e-02 4.00e+02 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 247 2.69 - 3.24: 8750 3.24 - 3.80: 14430 3.80 - 4.35: 20153 4.35 - 4.90: 31567 Nonbonded interactions: 75147 Sorted by model distance: nonbonded pdb=" OD2 ASP A 112 " pdb=" O HOH A 301 " model vdw 2.140 2.440 nonbonded pdb=" OD2 ASP D 112 " pdb=" O HOH D 301 " model vdw 2.161 2.440 nonbonded pdb=" OD2 ASP C 112 " pdb=" O HOH C 301 " model vdw 2.168 2.440 nonbonded pdb=" O VAL C 237 " pdb=" O HOH C 302 " model vdw 2.179 2.440 nonbonded pdb=" O VAL A 237 " pdb=" O HOH A 302 " model vdw 2.180 2.440 ... (remaining 75142 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' and (resid 13 through 19 or resid 21 through 33 or resid 35 through 3 \ 6 or resid 38 through 39 or resid 41 through 44 or resid 46 through 82 or resid \ 85 through 89 or resid 91 through 116 or resid 118 through 146 or resid 149 thro \ ugh 180 or resid 182 through 188 or resid 190 through 202 or resid 220 through 2 \ 24 or resid 226 through 237 or resid 239 through 256 or resid 258 through 282)) selection = (chain 'B' and (resid 13 through 19 or resid 21 through 33 or resid 35 through 3 \ 6 or resid 38 through 39 or resid 41 through 44 or resid 46 through 82 or resid \ 85 through 89 or resid 91 through 116 or resid 118 through 146 or resid 149 thro \ ugh 180 or resid 182 through 188 or resid 190 through 202 or resid 220 through 2 \ 24 or resid 226 through 237 or resid 239 through 256 or resid 258 through 282)) selection = (chain 'C' and (resid 13 through 19 or resid 21 through 33 or resid 35 through 3 \ 6 or resid 38 through 39 or resid 41 through 44 or resid 46 through 82 or resid \ 85 through 89 or resid 91 through 116 or resid 118 through 146 or resid 149 thro \ ugh 180 or resid 182 through 188 or resid 190 through 202 or resid 220 through 2 \ 24 or resid 226 through 237 or resid 239 through 256 or resid 258 through 282)) selection = (chain 'D' and (resid 13 through 19 or resid 21 through 33 or resid 35 through 3 \ 6 or resid 38 through 39 or resid 41 through 44 or resid 46 through 82 or resid \ 85 through 89 or resid 91 through 116 or resid 118 through 146 or resid 149 thro \ ugh 180 or resid 182 through 188 or resid 190 through 202 or resid 220 through 2 \ 24 or resid 226 through 237 or resid 239 through 256 or resid 258 through 282)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.96 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: 2.970 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: 12.160 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 29.950 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 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:11.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 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 : 0.008 0.050 8168 Z= 0.537 Angle : 0.594 5.284 11080 Z= 0.334 Chirality : 0.049 0.135 1264 Planarity : 0.005 0.052 1468 Dihedral : 11.733 81.046 3002 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 0.93 % 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: -0.54 (0.23), residues: 1117 helix: -0.01 (0.22), residues: 511 sheet: 0.38 (0.39), residues: 176 loop : -0.96 (0.26), residues: 430 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 0.790 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 113 average time/residue: 1.9066 time to fit residues: 224.4894 Evaluate side-chains 79 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.805 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.0629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 25 optimal weight: 0.0670 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 0.2980 chunk 58 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN B 235 GLN C 235 GLN D 233 ASN D 235 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8168 Z= 0.182 Angle : 0.501 8.810 11080 Z= 0.275 Chirality : 0.043 0.140 1264 Planarity : 0.004 0.050 1468 Dihedral : 4.042 14.222 1172 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 0.35 % 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: 0.92 (0.25), residues: 1117 helix: 1.37 (0.22), residues: 535 sheet: 0.48 (0.37), residues: 180 loop : -0.25 (0.31), residues: 402 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.906 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 81 average time/residue: 1.6093 time to fit residues: 137.4444 Evaluate side-chains 73 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.882 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 90 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 GLN C 235 GLN D 233 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 8168 Z= 0.189 Angle : 0.463 8.647 11080 Z= 0.252 Chirality : 0.043 0.166 1264 Planarity : 0.003 0.047 1468 Dihedral : 3.831 15.369 1172 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 0.58 % 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: 1.43 (0.26), residues: 1117 helix: 1.82 (0.22), residues: 535 sheet: 0.54 (0.37), residues: 182 loop : 0.06 (0.33), residues: 400 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 83 average time/residue: 1.7128 time to fit residues: 149.5019 Evaluate side-chains 79 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.917 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 GLN C 235 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 8168 Z= 0.249 Angle : 0.478 9.537 11080 Z= 0.260 Chirality : 0.043 0.154 1264 Planarity : 0.003 0.044 1468 Dihedral : 3.871 15.982 1172 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 0.58 % 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: 1.57 (0.26), residues: 1117 helix: 1.90 (0.22), residues: 535 sheet: 0.53 (0.37), residues: 182 loop : 0.22 (0.34), residues: 400 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.956 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 78 average time/residue: 1.6376 time to fit residues: 134.5470 Evaluate side-chains 76 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.807 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 8168 Z= 0.249 Angle : 0.467 7.396 11080 Z= 0.254 Chirality : 0.043 0.143 1264 Planarity : 0.003 0.044 1468 Dihedral : 3.848 16.745 1172 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 0.12 % 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: 1.69 (0.26), residues: 1117 helix: 1.99 (0.22), residues: 535 sheet: 0.56 (0.37), residues: 183 loop : 0.31 (0.34), residues: 399 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.886 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 78 average time/residue: 1.7324 time to fit residues: 142.2589 Evaluate side-chains 77 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN D 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 8168 Z= 0.300 Angle : 0.488 7.938 11080 Z= 0.265 Chirality : 0.043 0.142 1264 Planarity : 0.003 0.045 1468 Dihedral : 3.932 17.664 1172 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 0.46 % 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: 1.65 (0.26), residues: 1117 helix: 1.98 (0.22), residues: 535 sheet: 0.49 (0.37), residues: 185 loop : 0.28 (0.34), residues: 397 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.855 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 79 average time/residue: 1.6674 time to fit residues: 138.7928 Evaluate side-chains 78 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.884 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 96 optimal weight: 0.0980 chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 0.0980 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 0.0000 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 8168 Z= 0.156 Angle : 0.436 7.859 11080 Z= 0.235 Chirality : 0.041 0.136 1264 Planarity : 0.003 0.045 1468 Dihedral : 3.712 17.730 1172 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 0.00 % 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: 1.88 (0.26), residues: 1117 helix: 2.21 (0.22), residues: 535 sheet: 0.58 (0.38), residues: 183 loop : 0.36 (0.34), residues: 399 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.907 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 80 average time/residue: 1.6580 time to fit residues: 139.7499 Evaluate side-chains 81 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 1.028 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 1.2162 time to fit residues: 3.7615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 10.0000 chunk 18 optimal weight: 0.0570 chunk 61 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 84 optimal weight: 0.0020 chunk 89 optimal weight: 0.1980 overall best weight: 0.2906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN D 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 8168 Z= 0.133 Angle : 0.424 6.661 11080 Z= 0.228 Chirality : 0.041 0.137 1264 Planarity : 0.003 0.046 1468 Dihedral : 3.572 17.464 1172 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 0.00 % 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: 2.06 (0.26), residues: 1117 helix: 2.36 (0.23), residues: 535 sheet: 0.64 (0.38), residues: 181 loop : 0.45 (0.34), residues: 401 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.904 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 1.6359 time to fit residues: 138.1112 Evaluate side-chains 79 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 58 optimal weight: 0.3980 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN D 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 8168 Z= 0.256 Angle : 0.474 9.020 11080 Z= 0.256 Chirality : 0.042 0.135 1264 Planarity : 0.003 0.042 1468 Dihedral : 3.806 19.087 1172 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 0.00 % 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: 1.92 (0.26), residues: 1117 helix: 2.21 (0.22), residues: 535 sheet: 0.49 (0.38), residues: 185 loop : 0.48 (0.34), residues: 397 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.930 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 1.5884 time to fit residues: 130.9972 Evaluate side-chains 78 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 84 optimal weight: 0.4980 chunk 24 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN D 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8168 Z= 0.168 Angle : 0.441 7.807 11080 Z= 0.238 Chirality : 0.041 0.142 1264 Planarity : 0.003 0.044 1468 Dihedral : 3.698 19.874 1172 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 0.12 % 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: 2.03 (0.26), residues: 1117 helix: 2.29 (0.22), residues: 535 sheet: 0.58 (0.38), residues: 183 loop : 0.53 (0.35), residues: 399 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.840 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 1.5712 time to fit residues: 130.7671 Evaluate side-chains 78 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.742 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 0.0870 chunk 79 optimal weight: 0.0050 chunk 33 optimal weight: 0.0030 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN D 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.102878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.075455 restraints weight = 133413.261| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 4.81 r_work: 0.2968 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 8168 Z= 0.133 Angle : 0.423 7.843 11080 Z= 0.227 Chirality : 0.041 0.165 1264 Planarity : 0.003 0.045 1468 Dihedral : 3.555 19.102 1172 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 0.00 % 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: 2.22 (0.27), residues: 1117 helix: 2.45 (0.23), residues: 535 sheet: 0.67 (0.38), residues: 181 loop : 0.61 (0.35), residues: 401 =============================================================================== Job complete usr+sys time: 3331.51 seconds wall clock time: 59 minutes 57.71 seconds (3597.71 seconds total)