Starting phenix.real_space_refine on Sat Aug 23 02:38:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgo_43216/08_2025/8vgo_43216.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgo_43216/08_2025/8vgo_43216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vgo_43216/08_2025/8vgo_43216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgo_43216/08_2025/8vgo_43216.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgo_43216/08_2025/8vgo_43216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgo_43216/08_2025/8vgo_43216.cif" } resolution = 2.6 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.004 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 70 5.16 5 C 5822 2.51 5 N 1502 2.21 5 O 1754 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9148 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1670 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "B" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1620 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 200} Chain: "G" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1284 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain breaks: 1 Chain: "H" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1670 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "I" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1284 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain breaks: 1 Chain: "L" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1620 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 200} Time building chain proxies: 1.96, per 1000 atoms: 0.21 Number of scatterers: 9148 At special positions: 0 Unit cell: (100.12, 126.319, 130.998, 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 70 16.00 O 1754 8.00 N 1502 7.00 C 5822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 11 " - pdb=" SG CYS A 151 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS A 144 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 80 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 167 " - pdb=" SG CYS G 183 " distance=2.03 Simple disulfide: pdb=" SG CYS H 11 " - pdb=" SG CYS H 151 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 108 " - pdb=" SG CYS H 153 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 201 " distance=2.03 Simple disulfide: pdb=" SG CYS H 221 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS I 167 " - pdb=" SG CYS I 183 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 40 " - pdb=" SG CYS L 165 " distance=2.03 Simple disulfide: pdb=" SG CYS L 80 " - pdb=" SG CYS L 171 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 215.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 22 sheets defined 28.9% alpha, 38.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.671A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 192 through 195 removed outlier: 3.631A pdb=" N GLY A 195 " --> pdb=" O SER A 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 192 through 195' Processing helix chain 'A' and resid 206 through 209 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'G' and resid 48 through 71 Processing helix chain 'G' and resid 79 through 84 Processing helix chain 'G' and resid 85 through 97 Processing helix chain 'G' and resid 98 through 102 Processing helix chain 'G' and resid 114 through 143 Processing helix chain 'G' and resid 152 through 157 Processing helix chain 'G' and resid 171 through 176 removed outlier: 3.698A pdb=" N ASN G 176 " --> pdb=" O SER G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 216 removed outlier: 5.106A pdb=" N ASN G 214 " --> pdb=" O GLY G 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.627A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 131 through 133 No H-bonds generated for 'chain 'H' and resid 131 through 133' Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 192 through 195 removed outlier: 3.628A pdb=" N GLY H 195 " --> pdb=" O SER H 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 192 through 195' Processing helix chain 'H' and resid 206 through 209 Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 79 through 84 Processing helix chain 'I' and resid 85 through 97 Processing helix chain 'I' and resid 98 through 102 Processing helix chain 'I' and resid 114 through 143 Processing helix chain 'I' and resid 152 through 157 Processing helix chain 'I' and resid 171 through 176 removed outlier: 3.696A pdb=" N ASN I 176 " --> pdb=" O SER I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 216 removed outlier: 5.103A pdb=" N ASN I 214 " --> pdb=" O GLY I 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 12 removed outlier: 4.068A pdb=" N ASN A 33 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N MET A 34 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 9 through 12 removed outlier: 7.037A pdb=" N CYS A 92 " --> pdb=" O TRP A 103 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N TRP A 103 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG A 94 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 128 removed outlier: 5.576A pdb=" N TYR A 181 " --> pdb=" O ASP A 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 135 through 136 removed outlier: 5.576A pdb=" N TYR A 181 " --> pdb=" O ASP A 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 156 through 159 removed outlier: 4.105A pdb=" N TYR A 199 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.431A pdb=" N TRP B 35 " --> pdb=" O TRP B 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 13 Processing sheet with id=AB1, first strand: chain 'B' and resid 114 through 118 removed outlier: 5.802A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AB4, first strand: chain 'H' and resid 9 through 12 removed outlier: 4.063A pdb=" N ASN H 33 " --> pdb=" O SER H 95 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 9 through 12 removed outlier: 7.036A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ARG H 94 " --> pdb=" O ASN H 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 124 through 128 removed outlier: 5.576A pdb=" N TYR H 181 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 135 through 136 removed outlier: 5.576A pdb=" N TYR H 181 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 156 through 159 removed outlier: 4.105A pdb=" N TYR H 199 " --> pdb=" O VAL H 216 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.421A pdb=" N TRP L 35 " --> pdb=" O TRP L 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AC3, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.800A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 153 through 154 548 hydrogen bonds defined for protein. 1410 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: 1.25 Time building geometry restraints manager: 0.75 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: 2842 1.34 - 1.46: 2162 1.46 - 1.58: 4266 1.58 - 1.70: 0 1.70 - 1.82: 98 Bond restraints: 9368 Sorted by residual: bond pdb=" CB ILE I 162 " pdb=" CG1 ILE I 162 " ideal model delta sigma weight residual 1.530 1.512 0.018 2.00e-02 2.50e+03 7.83e-01 bond pdb=" CB ILE G 162 " pdb=" CG1 ILE G 162 " ideal model delta sigma weight residual 1.530 1.513 0.017 2.00e-02 2.50e+03 7.18e-01 bond pdb=" CB GLU G 150 " pdb=" CG GLU G 150 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.03e-01 bond pdb=" CB GLU I 150 " pdb=" CG GLU I 150 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.88e-01 bond pdb=" CB VAL L 19 " pdb=" CG1 VAL L 19 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.34e-01 ... (remaining 9363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 12024 1.30 - 2.60: 572 2.60 - 3.90: 104 3.90 - 5.20: 13 5.20 - 6.50: 17 Bond angle restraints: 12730 Sorted by residual: angle pdb=" C PHE A 150 " pdb=" N CYS A 151 " pdb=" CA CYS A 151 " ideal model delta sigma weight residual 121.54 128.04 -6.50 1.91e+00 2.74e-01 1.16e+01 angle pdb=" C PHE H 150 " pdb=" N CYS H 151 " pdb=" CA CYS H 151 " ideal model delta sigma weight residual 121.54 128.04 -6.50 1.91e+00 2.74e-01 1.16e+01 angle pdb=" CA TYR G 182 " pdb=" CB TYR G 182 " pdb=" CG TYR G 182 " ideal model delta sigma weight residual 113.90 119.58 -5.68 1.80e+00 3.09e-01 9.95e+00 angle pdb=" CA TYR I 182 " pdb=" CB TYR I 182 " pdb=" CG TYR I 182 " ideal model delta sigma weight residual 113.90 119.54 -5.64 1.80e+00 3.09e-01 9.83e+00 angle pdb=" C SER L 26 " pdb=" N SER L 28 " pdb=" CA SER L 28 " ideal model delta sigma weight residual 121.54 127.47 -5.93 1.91e+00 2.74e-01 9.63e+00 ... (remaining 12725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 5163 17.55 - 35.09: 375 35.09 - 52.64: 43 52.64 - 70.19: 21 70.19 - 87.74: 16 Dihedral angle restraints: 5618 sinusoidal: 2134 harmonic: 3484 Sorted by residual: dihedral pdb=" CA PHE H 150 " pdb=" C PHE H 150 " pdb=" N CYS H 151 " pdb=" CA CYS H 151 " ideal model delta harmonic sigma weight residual -180.00 -153.78 -26.22 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA PHE A 150 " pdb=" C PHE A 150 " pdb=" N CYS A 151 " pdb=" CA CYS A 151 " ideal model delta harmonic sigma weight residual 180.00 -153.85 -26.15 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA LYS H 219 " pdb=" C LYS H 219 " pdb=" N SER H 220 " pdb=" CA SER H 220 " ideal model delta harmonic sigma weight residual 180.00 153.85 26.15 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 5615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 766 0.029 - 0.058: 422 0.058 - 0.086: 150 0.086 - 0.115: 82 0.115 - 0.144: 22 Chirality restraints: 1442 Sorted by residual: chirality pdb=" CA ILE L 2 " pdb=" N ILE L 2 " pdb=" C ILE L 2 " pdb=" CB ILE L 2 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA ILE B 2 " pdb=" N ILE B 2 " pdb=" C ILE B 2 " pdb=" CB ILE B 2 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CB ILE G 162 " pdb=" CA ILE G 162 " pdb=" CG1 ILE G 162 " pdb=" CG2 ILE G 162 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 1439 not shown) Planarity restraints: 1594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 77 " 0.364 9.50e-02 1.11e+02 1.65e-01 2.11e+01 pdb=" NE ARG B 77 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG B 77 " 0.034 2.00e-02 2.50e+03 pdb=" NH1 ARG B 77 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG B 77 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 77 " -0.365 9.50e-02 1.11e+02 1.65e-01 2.10e+01 pdb=" NE ARG L 77 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG L 77 " -0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG L 77 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG L 77 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 52 " 0.001 2.00e-02 2.50e+03 2.97e-02 1.77e+01 pdb=" CG TYR A 52 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR A 52 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR A 52 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 52 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR A 52 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 52 " -0.042 2.00e-02 2.50e+03 pdb=" OH TYR A 52 " 0.042 2.00e-02 2.50e+03 ... (remaining 1591 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2790 2.83 - 3.35: 8686 3.35 - 3.86: 16018 3.86 - 4.38: 19300 4.38 - 4.90: 32252 Nonbonded interactions: 79046 Sorted by model distance: nonbonded pdb=" OE1 GLU L 105 " pdb=" OH TYR L 173 " model vdw 2.309 3.040 nonbonded pdb=" OE1 GLU B 105 " pdb=" OH TYR B 173 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR H 97 " pdb=" OE1 GLU I 174 " model vdw 2.312 3.040 nonbonded pdb=" NZ LYS H 215 " pdb=" OE1 GLU H 217 " model vdw 2.320 3.120 nonbonded pdb=" NZ LYS A 215 " pdb=" OE1 GLU A 217 " model vdw 2.322 3.120 ... (remaining 79041 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.490 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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 : 0.003 0.041 9388 Z= 0.138 Angle : 0.678 6.503 12770 Z= 0.375 Chirality : 0.044 0.144 1442 Planarity : 0.008 0.165 1594 Dihedral : 13.676 87.737 3330 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.79 % Favored : 94.71 % Rotamer: Outliers : 0.19 % Allowed : 2.53 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.24), residues: 1190 helix: -1.16 (0.25), residues: 270 sheet: 0.80 (0.24), residues: 418 loop : -0.34 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.005 ARG B 77 TYR 0.042 0.005 TYR A 52 PHE 0.027 0.002 PHE H 100D TRP 0.026 0.002 TRP G 89 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9368) covalent geometry : angle 0.67618 (12730) SS BOND : bond 0.00289 ( 20) SS BOND : angle 1.05451 ( 40) hydrogen bonds : bond 0.19913 ( 502) hydrogen bonds : angle 8.46989 ( 1410) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 220 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.8144 (tt0) cc_final: 0.7943 (tm-30) REVERT: G 76 ILE cc_start: 0.7825 (mt) cc_final: 0.7546 (tp) REVERT: G 137 ASP cc_start: 0.7669 (m-30) cc_final: 0.7168 (m-30) REVERT: G 203 PHE cc_start: 0.8010 (t80) cc_final: 0.7737 (t80) REVERT: I 76 ILE cc_start: 0.7824 (mt) cc_final: 0.7536 (tp) REVERT: I 85 TRP cc_start: 0.8183 (m100) cc_final: 0.7979 (m100) REVERT: I 137 ASP cc_start: 0.7611 (m-30) cc_final: 0.7136 (m-30) REVERT: I 203 PHE cc_start: 0.8012 (t80) cc_final: 0.7705 (t80) REVERT: L 17 GLU cc_start: 0.8605 (tt0) cc_final: 0.8386 (tt0) outliers start: 2 outliers final: 0 residues processed: 221 average time/residue: 0.6073 time to fit residues: 141.6898 Evaluate side-chains 148 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.0670 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN B 138 ASN G 56 GLN G 171 ASN H 202 ASN I 56 GLN I 171 ASN L 138 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.105457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.072200 restraints weight = 15118.974| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.50 r_work: 0.2811 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9388 Z= 0.182 Angle : 0.661 6.655 12770 Z= 0.353 Chirality : 0.045 0.151 1442 Planarity : 0.005 0.054 1594 Dihedral : 5.773 40.769 1280 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.18 % Favored : 98.66 % Rotamer: Outliers : 1.36 % Allowed : 10.99 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.24), residues: 1190 helix: 1.12 (0.31), residues: 268 sheet: 1.01 (0.23), residues: 424 loop : 0.23 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 24 TYR 0.018 0.002 TYR H 98 PHE 0.020 0.002 PHE A 100D TRP 0.024 0.002 TRP G 89 HIS 0.003 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 9368) covalent geometry : angle 0.65968 (12730) SS BOND : bond 0.00315 ( 20) SS BOND : angle 1.08753 ( 40) hydrogen bonds : bond 0.04402 ( 502) hydrogen bonds : angle 5.49518 ( 1410) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8831 (tt0) cc_final: 0.8584 (tm-30) REVERT: A 152 GLU cc_start: 0.8210 (tt0) cc_final: 0.7867 (tm-30) REVERT: B 123 GLU cc_start: 0.8368 (mp0) cc_final: 0.8163 (mp0) REVERT: B 147 GLN cc_start: 0.9072 (tp40) cc_final: 0.8822 (mt0) REVERT: B 187 GLU cc_start: 0.9258 (mt-10) cc_final: 0.9055 (mm-30) REVERT: G 76 ILE cc_start: 0.7959 (mt) cc_final: 0.7692 (tp) REVERT: G 117 MET cc_start: 0.6009 (tmm) cc_final: 0.5544 (mtt) REVERT: G 137 ASP cc_start: 0.7680 (m-30) cc_final: 0.7089 (m-30) REVERT: G 203 PHE cc_start: 0.7721 (t80) cc_final: 0.7449 (t80) REVERT: H 3 GLN cc_start: 0.8811 (tt0) cc_final: 0.8565 (tm-30) REVERT: H 152 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7663 (tm-30) REVERT: I 46 MET cc_start: 0.4030 (tpt) cc_final: 0.2787 (tmm) REVERT: I 76 ILE cc_start: 0.8110 (mt) cc_final: 0.7754 (tp) REVERT: I 85 TRP cc_start: 0.8230 (m100) cc_final: 0.8020 (m100) REVERT: I 117 MET cc_start: 0.6024 (tmm) cc_final: 0.5512 (mtt) REVERT: I 137 ASP cc_start: 0.7625 (m-30) cc_final: 0.7021 (m-30) REVERT: I 203 PHE cc_start: 0.7734 (t80) cc_final: 0.7454 (t80) REVERT: L 123 GLU cc_start: 0.8356 (mp0) cc_final: 0.8151 (mp0) REVERT: L 147 GLN cc_start: 0.9086 (tp40) cc_final: 0.8855 (mt0) REVERT: L 187 GLU cc_start: 0.9251 (mt-10) cc_final: 0.9031 (mm-30) outliers start: 14 outliers final: 4 residues processed: 156 average time/residue: 0.6246 time to fit residues: 103.4572 Evaluate side-chains 149 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 145 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 40 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN G 56 GLN H 3 GLN H 204 ASN I 56 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.102184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.068404 restraints weight = 14982.182| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.51 r_work: 0.2769 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 9388 Z= 0.286 Angle : 0.679 6.206 12770 Z= 0.362 Chirality : 0.047 0.199 1442 Planarity : 0.005 0.040 1594 Dihedral : 5.685 38.082 1280 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 2.53 % Allowed : 11.58 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.24), residues: 1190 helix: 1.13 (0.31), residues: 280 sheet: 1.04 (0.24), residues: 422 loop : 0.02 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 142 TYR 0.020 0.002 TYR A 98 PHE 0.019 0.002 PHE H 100D TRP 0.026 0.002 TRP G 89 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00669 ( 9368) covalent geometry : angle 0.67648 (12730) SS BOND : bond 0.00416 ( 20) SS BOND : angle 1.28938 ( 40) hydrogen bonds : bond 0.04592 ( 502) hydrogen bonds : angle 5.44623 ( 1410) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.8212 (tt0) cc_final: 0.7906 (tm-30) REVERT: B 123 GLU cc_start: 0.8345 (mp0) cc_final: 0.8098 (mp0) REVERT: B 142 ARG cc_start: 0.8607 (ttt-90) cc_final: 0.7851 (tmt170) REVERT: B 147 GLN cc_start: 0.9018 (tp40) cc_final: 0.8756 (mt0) REVERT: B 170 ASP cc_start: 0.8008 (t0) cc_final: 0.7607 (t0) REVERT: G 137 ASP cc_start: 0.7580 (m-30) cc_final: 0.7049 (m-30) REVERT: G 203 PHE cc_start: 0.7854 (t80) cc_final: 0.7601 (t80) REVERT: H 152 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7788 (tm-30) REVERT: I 76 ILE cc_start: 0.8140 (mt) cc_final: 0.7907 (tp) REVERT: I 137 ASP cc_start: 0.7608 (m-30) cc_final: 0.7206 (m-30) REVERT: I 203 PHE cc_start: 0.7867 (t80) cc_final: 0.7607 (t80) REVERT: L 123 GLU cc_start: 0.8341 (mp0) cc_final: 0.8093 (mp0) REVERT: L 142 ARG cc_start: 0.8616 (ttt-90) cc_final: 0.7845 (tmt170) REVERT: L 147 GLN cc_start: 0.9063 (tt0) cc_final: 0.8804 (mt0) REVERT: L 170 ASP cc_start: 0.8016 (t0) cc_final: 0.7608 (t0) outliers start: 26 outliers final: 5 residues processed: 166 average time/residue: 0.6156 time to fit residues: 108.5180 Evaluate side-chains 142 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 162 ILE Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 27 optimal weight: 0.0870 chunk 54 optimal weight: 0.4980 chunk 106 optimal weight: 0.6980 chunk 65 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 204 ASN G 56 GLN H 202 ASN H 204 ASN I 56 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.103869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.070199 restraints weight = 15122.846| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.51 r_work: 0.2804 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9388 Z= 0.142 Angle : 0.611 6.651 12770 Z= 0.322 Chirality : 0.043 0.181 1442 Planarity : 0.005 0.056 1594 Dihedral : 5.204 31.220 1280 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.53 % Allowed : 13.23 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.24), residues: 1190 helix: 1.43 (0.31), residues: 282 sheet: 1.17 (0.24), residues: 422 loop : 0.05 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 24 TYR 0.020 0.001 TYR I 182 PHE 0.015 0.001 PHE A 100D TRP 0.024 0.002 TRP G 89 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9368) covalent geometry : angle 0.60896 (12730) SS BOND : bond 0.00304 ( 20) SS BOND : angle 1.05382 ( 40) hydrogen bonds : bond 0.03820 ( 502) hydrogen bonds : angle 5.03927 ( 1410) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.378 Fit side-chains REVERT: A 5 GLN cc_start: 0.8621 (mm110) cc_final: 0.8156 (tp40) REVERT: A 152 GLU cc_start: 0.7996 (tt0) cc_final: 0.7658 (tm-30) REVERT: B 123 GLU cc_start: 0.8218 (mp0) cc_final: 0.7955 (mp0) REVERT: B 142 ARG cc_start: 0.8623 (ttt-90) cc_final: 0.7706 (tmt170) REVERT: B 147 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8689 (mt0) REVERT: B 183 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7709 (tttm) REVERT: G 117 MET cc_start: 0.5969 (tmm) cc_final: 0.5407 (mtt) REVERT: G 137 ASP cc_start: 0.7495 (m-30) cc_final: 0.6960 (m-30) REVERT: G 203 PHE cc_start: 0.7573 (t80) cc_final: 0.7285 (t80) REVERT: H 5 GLN cc_start: 0.8623 (mm110) cc_final: 0.8393 (mm110) REVERT: H 152 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7703 (tm-30) REVERT: I 76 ILE cc_start: 0.7924 (mt) cc_final: 0.7613 (tp) REVERT: I 117 MET cc_start: 0.5913 (tmm) cc_final: 0.5316 (mtt) REVERT: I 137 ASP cc_start: 0.7612 (m-30) cc_final: 0.6958 (m-30) REVERT: I 203 PHE cc_start: 0.7529 (t80) cc_final: 0.7238 (t80) REVERT: L 123 GLU cc_start: 0.8223 (mp0) cc_final: 0.7960 (mp0) REVERT: L 142 ARG cc_start: 0.8618 (ttt-90) cc_final: 0.7698 (tmt170) REVERT: L 147 GLN cc_start: 0.8954 (tt0) cc_final: 0.8708 (mt0) REVERT: L 183 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7707 (tttm) outliers start: 26 outliers final: 2 residues processed: 158 average time/residue: 0.6456 time to fit residues: 108.2202 Evaluate side-chains 142 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 183 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 102 optimal weight: 0.1980 chunk 33 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 100 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 204 ASN G 56 GLN H 5 GLN H 204 ASN I 56 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.105285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.071634 restraints weight = 14992.077| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.50 r_work: 0.2824 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9388 Z= 0.136 Angle : 0.592 6.778 12770 Z= 0.312 Chirality : 0.043 0.152 1442 Planarity : 0.004 0.036 1594 Dihedral : 5.002 25.204 1280 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.75 % Allowed : 14.79 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.25), residues: 1190 helix: 1.79 (0.31), residues: 272 sheet: 1.30 (0.24), residues: 428 loop : 0.18 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 142 TYR 0.019 0.001 TYR G 182 PHE 0.013 0.001 PHE H 100D TRP 0.025 0.001 TRP G 89 HIS 0.002 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9368) covalent geometry : angle 0.58999 (12730) SS BOND : bond 0.00244 ( 20) SS BOND : angle 0.97330 ( 40) hydrogen bonds : bond 0.03727 ( 502) hydrogen bonds : angle 4.93733 ( 1410) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.431 Fit side-chains REVERT: A 5 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8468 (mm110) REVERT: A 152 GLU cc_start: 0.8031 (tt0) cc_final: 0.7678 (tm-30) REVERT: B 40 CYS cc_start: 0.7973 (m) cc_final: 0.7646 (m) REVERT: B 123 GLU cc_start: 0.8269 (mp0) cc_final: 0.8005 (mp0) REVERT: B 142 ARG cc_start: 0.8639 (ttt-90) cc_final: 0.7740 (tmt170) REVERT: B 147 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8667 (mt0) REVERT: G 137 ASP cc_start: 0.7606 (m-30) cc_final: 0.6960 (m-30) REVERT: G 203 PHE cc_start: 0.7560 (t80) cc_final: 0.7286 (t80) REVERT: H 152 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7732 (tm-30) REVERT: I 137 ASP cc_start: 0.7534 (m-30) cc_final: 0.7064 (m-30) REVERT: I 203 PHE cc_start: 0.7524 (t80) cc_final: 0.7202 (t80) REVERT: L 123 GLU cc_start: 0.8274 (mp0) cc_final: 0.8013 (mp0) REVERT: L 142 ARG cc_start: 0.8636 (ttt-90) cc_final: 0.7724 (tmt170) REVERT: L 147 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8713 (mt0) outliers start: 18 outliers final: 3 residues processed: 153 average time/residue: 0.6927 time to fit residues: 112.1316 Evaluate side-chains 143 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 138 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 89 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN G 56 GLN H 3 GLN H 5 GLN H 204 ASN I 56 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.107871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.076710 restraints weight = 16113.368| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.45 r_work: 0.3048 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9388 Z= 0.200 Angle : 0.638 8.532 12770 Z= 0.334 Chirality : 0.044 0.158 1442 Planarity : 0.005 0.066 1594 Dihedral : 5.078 20.978 1280 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.43 % Allowed : 14.88 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.24), residues: 1190 helix: 1.71 (0.31), residues: 272 sheet: 1.26 (0.24), residues: 428 loop : 0.10 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 24 TYR 0.017 0.002 TYR G 86 PHE 0.015 0.002 PHE H 100D TRP 0.025 0.002 TRP G 89 HIS 0.002 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 9368) covalent geometry : angle 0.63605 (12730) SS BOND : bond 0.00280 ( 20) SS BOND : angle 1.16522 ( 40) hydrogen bonds : bond 0.03956 ( 502) hydrogen bonds : angle 5.08511 ( 1410) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.382 Fit side-chains REVERT: B 123 GLU cc_start: 0.8446 (mp0) cc_final: 0.8177 (mp0) REVERT: B 147 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8730 (mt0) REVERT: G 117 MET cc_start: 0.6294 (tmm) cc_final: 0.5685 (mtt) REVERT: G 137 ASP cc_start: 0.7653 (m-30) cc_final: 0.7196 (m-30) REVERT: G 203 PHE cc_start: 0.7854 (t80) cc_final: 0.7586 (t80) REVERT: H 3 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8398 (tm-30) REVERT: H 5 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8325 (mm110) REVERT: H 152 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7783 (tm-30) REVERT: I 117 MET cc_start: 0.6278 (tmm) cc_final: 0.5664 (mtt) REVERT: I 137 ASP cc_start: 0.7631 (m-30) cc_final: 0.7214 (m-30) REVERT: I 203 PHE cc_start: 0.7811 (t80) cc_final: 0.7540 (t80) REVERT: L 40 CYS cc_start: 0.8214 (m) cc_final: 0.7917 (m) REVERT: L 123 GLU cc_start: 0.8432 (mp0) cc_final: 0.8160 (mp0) REVERT: L 147 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8776 (mt0) outliers start: 25 outliers final: 8 residues processed: 149 average time/residue: 0.6788 time to fit residues: 107.2215 Evaluate side-chains 143 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 CYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 77 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 76 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 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 5 GLN A 204 ASN G 56 GLN H 3 GLN H 202 ASN H 204 ASN I 56 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.109192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.078153 restraints weight = 16126.103| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.46 r_work: 0.3076 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9388 Z= 0.150 Angle : 0.618 8.418 12770 Z= 0.323 Chirality : 0.043 0.159 1442 Planarity : 0.004 0.048 1594 Dihedral : 4.901 18.228 1280 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.24 % Allowed : 15.76 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.25), residues: 1190 helix: 1.79 (0.31), residues: 272 sheet: 1.31 (0.24), residues: 428 loop : 0.11 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 24 TYR 0.016 0.001 TYR G 86 PHE 0.013 0.001 PHE A 100D TRP 0.025 0.002 TRP G 89 HIS 0.002 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9368) covalent geometry : angle 0.61633 (12730) SS BOND : bond 0.00240 ( 20) SS BOND : angle 1.01834 ( 40) hydrogen bonds : bond 0.03710 ( 502) hydrogen bonds : angle 4.95319 ( 1410) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.375 Fit side-chains REVERT: B 123 GLU cc_start: 0.8418 (mp0) cc_final: 0.8151 (mp0) REVERT: B 142 ARG cc_start: 0.8562 (ttt-90) cc_final: 0.7859 (tmt170) REVERT: B 147 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8674 (mt0) REVERT: G 117 MET cc_start: 0.6239 (tmm) cc_final: 0.5618 (mtt) REVERT: G 137 ASP cc_start: 0.7638 (m-30) cc_final: 0.7189 (m-30) REVERT: G 203 PHE cc_start: 0.7781 (t80) cc_final: 0.7510 (t80) REVERT: H 152 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7840 (tm-30) REVERT: I 117 MET cc_start: 0.6165 (tmm) cc_final: 0.5546 (mtt) REVERT: I 137 ASP cc_start: 0.7663 (m-30) cc_final: 0.7216 (m-30) REVERT: I 203 PHE cc_start: 0.7741 (t80) cc_final: 0.7431 (t80) REVERT: L 123 GLU cc_start: 0.8406 (mp0) cc_final: 0.8142 (mp0) REVERT: L 142 ARG cc_start: 0.8555 (ttt-90) cc_final: 0.7848 (tmt170) REVERT: L 147 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8722 (mt0) outliers start: 23 outliers final: 10 residues processed: 148 average time/residue: 0.6469 time to fit residues: 101.5755 Evaluate side-chains 142 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 CYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 87 optimal weight: 0.3980 chunk 91 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 202 ASN A 204 ASN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 5 GLN H 204 ASN I 56 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.108513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.077412 restraints weight = 15918.569| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.44 r_work: 0.3065 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9388 Z= 0.171 Angle : 0.636 8.062 12770 Z= 0.332 Chirality : 0.043 0.151 1442 Planarity : 0.005 0.077 1594 Dihedral : 4.906 17.905 1280 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.85 % Allowed : 16.63 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.25), residues: 1190 helix: 1.82 (0.31), residues: 270 sheet: 1.31 (0.24), residues: 428 loop : 0.10 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG B 24 TYR 0.017 0.001 TYR G 86 PHE 0.014 0.002 PHE H 100D TRP 0.024 0.002 TRP I 89 HIS 0.002 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9368) covalent geometry : angle 0.63370 (12730) SS BOND : bond 0.00266 ( 20) SS BOND : angle 1.07005 ( 40) hydrogen bonds : bond 0.03811 ( 502) hydrogen bonds : angle 4.98462 ( 1410) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.267 Fit side-chains REVERT: B 123 GLU cc_start: 0.8439 (mp0) cc_final: 0.8185 (mp0) REVERT: B 142 ARG cc_start: 0.8579 (ttt-90) cc_final: 0.7831 (tmt170) REVERT: B 147 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8676 (mt0) REVERT: G 117 MET cc_start: 0.6236 (tmm) cc_final: 0.5689 (mtt) REVERT: G 137 ASP cc_start: 0.7664 (m-30) cc_final: 0.7207 (m-30) REVERT: G 203 PHE cc_start: 0.7837 (t80) cc_final: 0.7571 (t80) REVERT: H 3 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8415 (tm-30) REVERT: H 5 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8297 (mm110) REVERT: H 152 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7849 (tm-30) REVERT: I 117 MET cc_start: 0.6215 (tmm) cc_final: 0.5652 (mtt) REVERT: I 137 ASP cc_start: 0.7667 (m-30) cc_final: 0.7237 (m-30) REVERT: I 203 PHE cc_start: 0.7809 (t80) cc_final: 0.7538 (t80) REVERT: L 123 GLU cc_start: 0.8423 (mp0) cc_final: 0.8171 (mp0) REVERT: L 142 ARG cc_start: 0.8562 (ttt-90) cc_final: 0.7816 (tmt170) REVERT: L 147 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8756 (mt0) outliers start: 19 outliers final: 10 residues processed: 147 average time/residue: 0.6781 time to fit residues: 105.6242 Evaluate side-chains 144 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 CYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 14 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 1 optimal weight: 0.0970 chunk 46 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 5 GLN A 204 ASN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 202 ASN H 204 ASN ** I 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.109288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.077961 restraints weight = 15898.599| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.47 r_work: 0.3072 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9388 Z= 0.162 Angle : 0.636 8.182 12770 Z= 0.332 Chirality : 0.043 0.151 1442 Planarity : 0.004 0.055 1594 Dihedral : 4.850 17.742 1280 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.75 % Allowed : 17.12 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.25), residues: 1190 helix: 1.82 (0.31), residues: 270 sheet: 1.35 (0.24), residues: 428 loop : 0.11 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 24 TYR 0.016 0.001 TYR G 86 PHE 0.014 0.001 PHE H 100D TRP 0.024 0.002 TRP I 89 HIS 0.002 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9368) covalent geometry : angle 0.63452 (12730) SS BOND : bond 0.00269 ( 20) SS BOND : angle 1.03446 ( 40) hydrogen bonds : bond 0.03758 ( 502) hydrogen bonds : angle 4.94570 ( 1410) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.388 Fit side-chains REVERT: A 5 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8375 (mm110) REVERT: B 123 GLU cc_start: 0.8444 (mp0) cc_final: 0.8191 (mp0) REVERT: B 142 ARG cc_start: 0.8689 (ttt-90) cc_final: 0.7864 (tmt170) REVERT: B 147 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8709 (mt0) REVERT: G 117 MET cc_start: 0.6362 (tmm) cc_final: 0.5654 (mtt) REVERT: G 137 ASP cc_start: 0.7661 (m-30) cc_final: 0.7218 (m-30) REVERT: G 203 PHE cc_start: 0.7853 (t80) cc_final: 0.7554 (t80) REVERT: H 3 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8483 (tm-30) REVERT: H 5 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8338 (mm110) REVERT: H 152 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7865 (tm-30) REVERT: I 117 MET cc_start: 0.6367 (tmm) cc_final: 0.5652 (mtt) REVERT: I 137 ASP cc_start: 0.7658 (m-30) cc_final: 0.7220 (m-30) REVERT: I 203 PHE cc_start: 0.7803 (t80) cc_final: 0.7517 (t80) REVERT: L 123 GLU cc_start: 0.8428 (mp0) cc_final: 0.8179 (mp0) REVERT: L 142 ARG cc_start: 0.8683 (ttt-90) cc_final: 0.7865 (tmt170) REVERT: L 147 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8765 (mt0) outliers start: 18 outliers final: 9 residues processed: 147 average time/residue: 0.6862 time to fit residues: 106.8276 Evaluate side-chains 143 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 CYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 48 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 0.0030 chunk 24 optimal weight: 0.7980 chunk 78 optimal weight: 0.0370 chunk 69 optimal weight: 0.4980 chunk 58 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 overall best weight: 0.2068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 ASN ** I 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.111656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.080671 restraints weight = 15982.441| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.48 r_work: 0.3126 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9388 Z= 0.117 Angle : 0.625 9.243 12770 Z= 0.325 Chirality : 0.042 0.158 1442 Planarity : 0.004 0.063 1594 Dihedral : 4.630 16.872 1280 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.46 % Allowed : 17.61 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.25), residues: 1190 helix: 1.92 (0.32), residues: 270 sheet: 1.46 (0.25), residues: 430 loop : 0.18 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 24 TYR 0.016 0.001 TYR G 86 PHE 0.012 0.001 PHE H 100D TRP 0.023 0.002 TRP I 89 HIS 0.002 0.000 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9368) covalent geometry : angle 0.62384 (12730) SS BOND : bond 0.00206 ( 20) SS BOND : angle 0.88045 ( 40) hydrogen bonds : bond 0.03477 ( 502) hydrogen bonds : angle 4.74110 ( 1410) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8266 (mm110) REVERT: B 123 GLU cc_start: 0.8439 (mp0) cc_final: 0.8192 (mp0) REVERT: B 142 ARG cc_start: 0.8675 (ttt-90) cc_final: 0.7955 (tmt170) REVERT: B 147 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8695 (mt0) REVERT: B 167 ASP cc_start: 0.8810 (t0) cc_final: 0.8593 (t0) REVERT: G 137 ASP cc_start: 0.7728 (m-30) cc_final: 0.7254 (m-30) REVERT: G 203 PHE cc_start: 0.7668 (t80) cc_final: 0.7406 (t80) REVERT: H 152 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7830 (tm-30) REVERT: I 137 ASP cc_start: 0.7748 (m-30) cc_final: 0.7139 (m-30) REVERT: I 203 PHE cc_start: 0.7716 (t80) cc_final: 0.7442 (t80) REVERT: L 123 GLU cc_start: 0.8423 (mp0) cc_final: 0.8180 (mp0) REVERT: L 142 ARG cc_start: 0.8636 (ttt-90) cc_final: 0.7937 (tmt170) REVERT: L 147 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8731 (mt0) outliers start: 15 outliers final: 9 residues processed: 158 average time/residue: 0.5946 time to fit residues: 99.8248 Evaluate side-chains 151 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 CYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 6 optimal weight: 0.4980 chunk 91 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 204 ASN ** I 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.108263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.076245 restraints weight = 15869.115| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.53 r_work: 0.3005 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9388 Z= 0.182 Angle : 0.664 9.512 12770 Z= 0.345 Chirality : 0.044 0.154 1442 Planarity : 0.005 0.063 1594 Dihedral : 4.806 17.762 1280 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.85 % Allowed : 18.29 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.25), residues: 1190 helix: 1.73 (0.31), residues: 270 sheet: 1.44 (0.24), residues: 428 loop : 0.18 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 24 TYR 0.018 0.002 TYR G 86 PHE 0.019 0.002 PHE G 62 TRP 0.021 0.002 TRP G 89 HIS 0.001 0.000 HIS G 63 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 9368) covalent geometry : angle 0.66212 (12730) SS BOND : bond 0.00336 ( 20) SS BOND : angle 1.09919 ( 40) hydrogen bonds : bond 0.03843 ( 502) hydrogen bonds : angle 4.93769 ( 1410) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4596.78 seconds wall clock time: 79 minutes 14.27 seconds (4754.27 seconds total)