Starting phenix.real_space_refine (version: dev) on Thu May 12 21:15:04 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6p_12739/05_2022/7o6p_12739.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6p_12739/05_2022/7o6p_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_12739/05_2022/7o6p_12739.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6p_12739/05_2022/7o6p_12739.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6p_12739/05_2022/7o6p_12739.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6p_12739/05_2022/7o6p_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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: 8.68, per 1000 atoms: 1.05 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: 3.60 Conformation dependent library (CDL) restraints added in 2.5 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: 2.41 Time building geometry restraints manager: 3.86 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 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. 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: 2.100 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: 11.790 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.070 Process input model: 31.400 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 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 : 0.850 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 113 average time/residue: 1.8645 time to fit residues: 219.8768 Evaluate side-chains 79 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.932 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.2176 ------------------------------------------------------------------------------- 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: 0.7980 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 0.2980 chunk 58 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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: 0.8712 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 8168 Z= 0.189 Angle : 0.500 8.590 11080 Z= 0.275 Chirality : 0.043 0.141 1264 Planarity : 0.004 0.049 1468 Dihedral : 4.045 14.270 1172 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 0.23 % 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: 0.95 (0.25), residues: 1117 helix: 1.39 (0.22), residues: 535 sheet: 0.61 (0.37), residues: 174 loop : -0.29 (0.31), residues: 408 *********************** 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 81 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 81 average time/residue: 1.5471 time to fit residues: 132.3311 Evaluate side-chains 74 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.969 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.2129 ------------------------------------------------------------------------------- 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: 0.6980 chunk 61 optimal weight: 0.5980 chunk 25 optimal weight: 0.0980 chunk 90 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8716 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8168 Z= 0.205 Angle : 0.468 7.959 11080 Z= 0.255 Chirality : 0.043 0.166 1264 Planarity : 0.003 0.046 1468 Dihedral : 3.865 15.040 1172 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.27 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: 1.42 (0.25), residues: 1117 helix: 1.82 (0.22), residues: 535 sheet: 0.52 (0.37), residues: 182 loop : 0.05 (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 85 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 82 average time/residue: 1.5289 time to fit residues: 132.4369 Evaluate side-chains 80 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.839 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.0555 ------------------------------------------------------------------------------- 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: 0.5980 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8736 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 8168 Z= 0.272 Angle : 0.488 8.589 11080 Z= 0.266 Chirality : 0.043 0.153 1264 Planarity : 0.003 0.045 1468 Dihedral : 3.912 17.821 1172 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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: 1.53 (0.26), residues: 1117 helix: 1.86 (0.22), residues: 535 sheet: 0.47 (0.36), residues: 184 loop : 0.23 (0.34), residues: 398 *********************** 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 80 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.964 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 78 average time/residue: 1.5234 time to fit residues: 125.4485 Evaluate side-chains 75 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.824 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.1683 ------------------------------------------------------------------------------- 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: 1.9990 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** C 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1829 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= 0.232 Angle : 0.464 7.836 11080 Z= 0.251 Chirality : 0.042 0.147 1264 Planarity : 0.003 0.045 1468 Dihedral : 3.839 17.504 1172 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 0.23 % 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: 1.68 (0.26), residues: 1117 helix: 1.99 (0.22), residues: 535 sheet: 0.57 (0.37), residues: 183 loop : 0.30 (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 79 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.882 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 78 average time/residue: 1.6175 time to fit residues: 133.0722 Evaluate side-chains 77 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.934 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.1504 ------------------------------------------------------------------------------- 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: 0.0770 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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: 0.8716 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8168 Z= 0.205 Angle : 0.451 7.684 11080 Z= 0.244 Chirality : 0.042 0.137 1264 Planarity : 0.003 0.045 1468 Dihedral : 3.765 17.291 1172 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: 1.78 (0.26), residues: 1117 helix: 2.08 (0.22), residues: 535 sheet: 0.56 (0.38), residues: 183 loop : 0.36 (0.34), residues: 399 *********************** 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 : 0.917 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 80 average time/residue: 1.5347 time to fit residues: 129.5738 Evaluate side-chains 78 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.1448 ------------------------------------------------------------------------------- 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: 0.9980 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 0.0050 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 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 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: 0.8728 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 8168 Z= 0.245 Angle : 0.468 9.343 11080 Z= 0.253 Chirality : 0.042 0.138 1264 Planarity : 0.003 0.044 1468 Dihedral : 3.820 18.098 1172 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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: 1.77 (0.26), residues: 1117 helix: 2.08 (0.22), residues: 535 sheet: 0.49 (0.37), residues: 185 loop : 0.39 (0.34), residues: 397 *********************** 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 81 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.981 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 79 average time/residue: 1.5675 time to fit residues: 130.5167 Evaluate side-chains 79 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.889 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.1569 ------------------------------------------------------------------------------- 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: 9.9990 chunk 18 optimal weight: 0.0570 chunk 61 optimal weight: 0.1980 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 overall best weight: 0.4098 ------------------------------------------------------------------------------- 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: 0.8697 moved from start: 0.2114 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= 0.159 Angle : 0.439 7.746 11080 Z= 0.236 Chirality : 0.041 0.134 1264 Planarity : 0.003 0.045 1468 Dihedral : 3.698 19.367 1172 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: 1.96 (0.26), residues: 1117 helix: 2.23 (0.22), residues: 535 sheet: 0.61 (0.38), residues: 183 loop : 0.45 (0.34), residues: 399 *********************** 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 81 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.922 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 2 residues processed: 81 average time/residue: 1.4928 time to fit residues: 127.9500 Evaluate side-chains 80 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.888 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 1.1028 time to fit residues: 2.3515 ------------------------------------------------------------------------------- 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: 0.5980 chunk 54 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 89 optimal weight: 0.1980 chunk 58 optimal weight: 0.2980 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.8704 moved from start: 0.2107 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= 0.181 Angle : 0.447 9.190 11080 Z= 0.239 Chirality : 0.041 0.138 1264 Planarity : 0.003 0.044 1468 Dihedral : 3.684 20.040 1172 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.46 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: 1.97 (0.26), residues: 1117 helix: 2.24 (0.22), residues: 535 sheet: 0.57 (0.38), residues: 183 loop : 0.49 (0.35), residues: 399 *********************** 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 81 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.923 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 80 average time/residue: 1.4724 time to fit residues: 124.5239 Evaluate side-chains 79 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.879 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.1519 ------------------------------------------------------------------------------- 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: 0.9990 chunk 99 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 0.0370 chunk 8 optimal weight: 0.0040 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 0.0060 chunk 24 optimal weight: 0.9980 overall best weight: 0.4086 ------------------------------------------------------------------------------- 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: 0.8691 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 8168 Z= 0.158 Angle : 0.432 7.530 11080 Z= 0.234 Chirality : 0.041 0.162 1264 Planarity : 0.003 0.044 1468 Dihedral : 3.631 21.028 1172 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: 2.06 (0.26), residues: 1117 helix: 2.33 (0.23), residues: 535 sheet: 0.54 (0.38), residues: 183 loop : 0.56 (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 78 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.945 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 78 average time/residue: 1.5126 time to fit residues: 124.6646 Evaluate side-chains 78 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.942 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.1869 ------------------------------------------------------------------------------- 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: 0.8980 chunk 22 optimal weight: 0.0970 chunk 79 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.100724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.073140 restraints weight = 132396.456| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 4.78 r_work: 0.3110 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work: 0.3026 rms_B_bonded: 4.39 restraints_weight: 0.1250 r_work: 0.2983 rms_B_bonded: 4.67 restraints_weight: 0.0625 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9166 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 8168 Z= 0.223 Angle : 0.454 7.845 11080 Z= 0.247 Chirality : 0.042 0.156 1264 Planarity : 0.003 0.043 1468 Dihedral : 3.739 21.914 1172 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: 1.99 (0.26), residues: 1117 helix: 2.25 (0.22), residues: 535 sheet: 0.43 (0.37), residues: 185 loop : 0.60 (0.35), residues: 397 =============================================================================== Job complete usr+sys time: 2923.82 seconds wall clock time: 52 minutes 56.52 seconds (3176.52 seconds total)