Starting phenix.real_space_refine on Sun Jun 8 03:22:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgo_43216/06_2025/8vgo_43216.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgo_43216/06_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_43216/06_2025/8vgo_43216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgo_43216/06_2025/8vgo_43216.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgo_43216/06_2025/8vgo_43216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgo_43216/06_2025/8vgo_43216.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.55, per 1000 atoms: 0.72 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: 2.13 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.26 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: 2.76 Time building geometry restraints manager: 2.57 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: 4.240 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.540 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.340 ------------------------------------------------------------------------------- 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 : 2.92 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.24), 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 TRP 0.026 0.002 TRP G 89 HIS 0.002 0.001 HIS H 35 PHE 0.027 0.002 PHE H 100D TYR 0.042 0.005 TYR A 52 ARG 0.038 0.005 ARG B 77 Details of bonding type rmsd hydrogen bonds : bond 0.19913 ( 502) hydrogen bonds : angle 8.46989 ( 1410) SS BOND : bond 0.00289 ( 20) SS BOND : angle 1.05451 ( 40) covalent geometry : bond 0.00321 ( 9368) covalent geometry : angle 0.67618 (12730) *********************** 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 : 0.973 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: 0.7584 (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: 1.4808 time to fit residues: 345.5148 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 : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 0.0670 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 47 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.106625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.073755 restraints weight = 15022.508| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.47 r_work: 0.2871 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9388 Z= 0.152 Angle : 0.648 6.604 12770 Z= 0.344 Chirality : 0.044 0.151 1442 Planarity : 0.005 0.050 1594 Dihedral : 5.682 39.563 1280 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.18 % Favored : 98.66 % Rotamer: Outliers : 1.36 % Allowed : 10.80 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 1.10 (0.24), residues: 1190 helix: 1.20 (0.31), residues: 268 sheet: 1.03 (0.23), residues: 424 loop : 0.34 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 89 HIS 0.003 0.001 HIS A 35 PHE 0.020 0.002 PHE A 100D TYR 0.018 0.002 TYR H 98 ARG 0.011 0.001 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 502) hydrogen bonds : angle 5.42166 ( 1410) SS BOND : bond 0.00279 ( 20) SS BOND : angle 0.99565 ( 40) covalent geometry : bond 0.00339 ( 9368) covalent geometry : angle 0.64627 (12730) *********************** 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 167 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8811 (tt0) cc_final: 0.8586 (tm-30) REVERT: A 152 GLU cc_start: 0.8226 (tt0) cc_final: 0.7876 (tm-30) REVERT: B 123 GLU cc_start: 0.8341 (mp0) cc_final: 0.8126 (mp0) REVERT: B 147 GLN cc_start: 0.9071 (tp40) cc_final: 0.8824 (mt0) REVERT: B 187 GLU cc_start: 0.9244 (mt-10) cc_final: 0.9041 (mm-30) REVERT: G 76 ILE cc_start: 0.7964 (mt) cc_final: 0.7683 (tp) REVERT: G 117 MET cc_start: 0.6026 (tmm) cc_final: 0.5547 (mtt) REVERT: G 137 ASP cc_start: 0.7669 (m-30) cc_final: 0.7065 (m-30) REVERT: G 203 PHE cc_start: 0.7680 (t80) cc_final: 0.7383 (t80) REVERT: H 3 GLN cc_start: 0.8793 (tt0) cc_final: 0.8576 (tm-30) REVERT: H 72 ASP cc_start: 0.8563 (t0) cc_final: 0.8230 (t0) REVERT: H 152 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7669 (tm-30) REVERT: I 76 ILE cc_start: 0.8116 (mt) cc_final: 0.7770 (tp) REVERT: I 85 TRP cc_start: 0.8209 (m100) cc_final: 0.7981 (m100) REVERT: I 117 MET cc_start: 0.6010 (tmm) cc_final: 0.5481 (mtt) REVERT: I 137 ASP cc_start: 0.7666 (m-30) cc_final: 0.7071 (m-30) REVERT: I 203 PHE cc_start: 0.7676 (t80) cc_final: 0.7390 (t80) REVERT: L 123 GLU cc_start: 0.8336 (mp0) cc_final: 0.8132 (mp0) REVERT: L 147 GLN cc_start: 0.9082 (tp40) cc_final: 0.8848 (mt0) REVERT: L 187 GLU cc_start: 0.9239 (mt-10) cc_final: 0.9031 (mm-30) outliers start: 14 outliers final: 4 residues processed: 157 average time/residue: 1.5338 time to fit residues: 258.3342 Evaluate side-chains 146 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 1.655 ------------------------------------------------------------------------------- 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 113 optimal weight: 0.1980 chunk 50 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 I 56 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.102210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.067756 restraints weight = 15333.681| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.57 r_work: 0.2776 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 9388 Z= 0.259 Angle : 0.665 6.175 12770 Z= 0.354 Chirality : 0.046 0.200 1442 Planarity : 0.005 0.039 1594 Dihedral : 5.580 36.225 1280 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.02 % Favored : 97.82 % Rotamer: Outliers : 2.24 % Allowed : 11.28 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 0.99 (0.24), residues: 1190 helix: 1.21 (0.31), residues: 280 sheet: 1.08 (0.24), residues: 422 loop : 0.06 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 89 HIS 0.003 0.001 HIS H 35 PHE 0.019 0.002 PHE H 100D TYR 0.020 0.002 TYR A 98 ARG 0.008 0.001 ARG L 142 Details of bonding type rmsd hydrogen bonds : bond 0.04474 ( 502) hydrogen bonds : angle 5.37177 ( 1410) SS BOND : bond 0.00381 ( 20) SS BOND : angle 1.27611 ( 40) covalent geometry : bond 0.00605 ( 9368) covalent geometry : angle 0.66231 (12730) *********************** 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 174 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.8218 (tt0) cc_final: 0.7892 (tm-30) REVERT: B 123 GLU cc_start: 0.8319 (mp0) cc_final: 0.8065 (mp0) REVERT: B 142 ARG cc_start: 0.8627 (ttt-90) cc_final: 0.7798 (tmt170) REVERT: B 147 GLN cc_start: 0.9038 (tp40) cc_final: 0.8768 (mt0) REVERT: B 170 ASP cc_start: 0.8004 (t0) cc_final: 0.7590 (t0) REVERT: G 76 ILE cc_start: 0.8117 (mt) cc_final: 0.7886 (tp) REVERT: G 137 ASP cc_start: 0.7533 (m-30) cc_final: 0.7112 (m-30) REVERT: G 203 PHE cc_start: 0.7820 (t80) cc_final: 0.7564 (t80) REVERT: H 152 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7748 (tm-30) REVERT: I 76 ILE cc_start: 0.8118 (mt) cc_final: 0.7866 (tp) REVERT: I 85 TRP cc_start: 0.8323 (m100) cc_final: 0.8094 (m100) REVERT: I 137 ASP cc_start: 0.7625 (m-30) cc_final: 0.7210 (m-30) REVERT: I 203 PHE cc_start: 0.7816 (t80) cc_final: 0.7535 (t80) REVERT: L 123 GLU cc_start: 0.8317 (mp0) cc_final: 0.8064 (mp0) REVERT: L 142 ARG cc_start: 0.8645 (ttt-90) cc_final: 0.7818 (tmt170) REVERT: L 147 GLN cc_start: 0.9082 (tt0) cc_final: 0.8837 (mt0) REVERT: L 170 ASP cc_start: 0.8015 (t0) cc_final: 0.7596 (t0) outliers start: 23 outliers final: 5 residues processed: 162 average time/residue: 1.9105 time to fit residues: 330.3553 Evaluate side-chains 148 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 1.872 ------------------------------------------------------------------------------- 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 95 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 27 optimal weight: 0.0980 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 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 5 GLN A 202 ASN A 204 ASN G 56 GLN H 5 GLN H 202 ASN H 204 ASN I 56 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.103764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.070055 restraints weight = 14855.010| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.49 r_work: 0.2802 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9388 Z= 0.154 Angle : 0.614 7.919 12770 Z= 0.323 Chirality : 0.043 0.173 1442 Planarity : 0.004 0.055 1594 Dihedral : 5.167 29.508 1280 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.24 % Allowed : 13.52 % 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 (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: 1.14 (0.24), residues: 1190 helix: 1.43 (0.31), residues: 282 sheet: 1.16 (0.24), residues: 422 loop : 0.06 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 89 HIS 0.002 0.001 HIS H 35 PHE 0.015 0.002 PHE H 100D TYR 0.016 0.001 TYR I 86 ARG 0.014 0.001 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 502) hydrogen bonds : angle 5.04312 ( 1410) SS BOND : bond 0.00240 ( 20) SS BOND : angle 1.03339 ( 40) covalent geometry : bond 0.00351 ( 9368) covalent geometry : angle 0.61222 (12730) *********************** 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 175 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 152 GLU cc_start: 0.8064 (tt0) cc_final: 0.7710 (tm-30) REVERT: B 123 GLU cc_start: 0.8243 (mp0) cc_final: 0.7974 (mp0) REVERT: B 142 ARG cc_start: 0.8626 (ttt-90) cc_final: 0.7710 (tmt170) REVERT: B 147 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8700 (mt0) REVERT: B 183 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7755 (tttm) REVERT: G 117 MET cc_start: 0.5961 (tmm) cc_final: 0.5451 (mtt) REVERT: G 137 ASP cc_start: 0.7597 (m-30) cc_final: 0.6939 (m-30) REVERT: G 203 PHE cc_start: 0.7619 (t80) cc_final: 0.7331 (t80) REVERT: H 152 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7741 (tm-30) REVERT: I 76 ILE cc_start: 0.7940 (mt) cc_final: 0.7703 (tp) REVERT: I 117 MET cc_start: 0.6000 (tmm) cc_final: 0.5423 (mtt) REVERT: I 137 ASP cc_start: 0.7655 (m-30) cc_final: 0.6994 (m-30) REVERT: I 203 PHE cc_start: 0.7588 (t80) cc_final: 0.7298 (t80) REVERT: L 123 GLU cc_start: 0.8241 (mp0) cc_final: 0.7973 (mp0) REVERT: L 142 ARG cc_start: 0.8622 (ttt-90) cc_final: 0.7705 (tmt170) REVERT: L 147 GLN cc_start: 0.8972 (tt0) cc_final: 0.8733 (mt0) REVERT: L 183 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7778 (tttm) outliers start: 23 outliers final: 2 residues processed: 164 average time/residue: 1.3050 time to fit residues: 227.8381 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 : 1.053 ------------------------------------------------------------------------------- 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 33 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 204 ASN G 56 GLN H 3 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 = 0.3608 r_free = 0.3608 target = 0.106322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.074005 restraints weight = 14960.146| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.38 r_work: 0.2867 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9388 Z= 0.182 Angle : 0.618 6.395 12770 Z= 0.327 Chirality : 0.044 0.148 1442 Planarity : 0.004 0.042 1594 Dihedral : 5.130 25.254 1280 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.11 % Favored : 96.81 % Rotamer: Outliers : 2.43 % Allowed : 13.72 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.24), residues: 1190 helix: 1.70 (0.31), residues: 272 sheet: 1.25 (0.24), residues: 420 loop : -0.01 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 89 HIS 0.002 0.001 HIS A 35 PHE 0.016 0.002 PHE G 62 TYR 0.019 0.002 TYR G 182 ARG 0.010 0.001 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 502) hydrogen bonds : angle 5.07523 ( 1410) SS BOND : bond 0.00266 ( 20) SS BOND : angle 1.08872 ( 40) covalent geometry : bond 0.00422 ( 9368) covalent geometry : angle 0.61630 (12730) *********************** 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 165 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.449 Fit side-chains REVERT: B 123 GLU cc_start: 0.8380 (mp0) cc_final: 0.8105 (mp0) REVERT: B 147 GLN cc_start: 0.9034 (tp40) cc_final: 0.8764 (mt0) REVERT: G 117 MET cc_start: 0.6197 (tmm) cc_final: 0.5593 (mtt) REVERT: G 137 ASP cc_start: 0.7596 (m-30) cc_final: 0.7143 (m-30) REVERT: G 203 PHE cc_start: 0.7789 (t80) cc_final: 0.7499 (t80) REVERT: H 3 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8493 (tm-30) REVERT: H 5 GLN cc_start: 0.8748 (mm110) cc_final: 0.8451 (mm110) REVERT: H 152 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7859 (tm-30) REVERT: I 137 ASP cc_start: 0.7630 (m-30) cc_final: 0.7206 (m-30) REVERT: I 203 PHE cc_start: 0.7785 (t80) cc_final: 0.7509 (t80) REVERT: L 40 CYS cc_start: 0.8090 (m) cc_final: 0.7801 (m) REVERT: L 123 GLU cc_start: 0.8385 (mp0) cc_final: 0.8112 (mp0) REVERT: L 147 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8829 (mt0) outliers start: 25 outliers final: 2 residues processed: 156 average time/residue: 1.4679 time to fit residues: 243.2564 Evaluate side-chains 142 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 138 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain H residue 3 GLN 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 6 optimal weight: 0.0970 chunk 20 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 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 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 = 0.3632 r_free = 0.3632 target = 0.108837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.077864 restraints weight = 15861.938| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.43 r_work: 0.3059 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9388 Z= 0.162 Angle : 0.628 8.512 12770 Z= 0.330 Chirality : 0.043 0.156 1442 Planarity : 0.004 0.069 1594 Dihedral : 5.027 20.211 1280 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.43 % Allowed : 14.69 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 1.29 (0.24), residues: 1190 helix: 1.78 (0.31), residues: 272 sheet: 1.22 (0.24), residues: 428 loop : 0.06 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 89 HIS 0.002 0.001 HIS A 35 PHE 0.014 0.001 PHE A 100D TYR 0.016 0.001 TYR I 86 ARG 0.015 0.002 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 502) hydrogen bonds : angle 4.97673 ( 1410) SS BOND : bond 0.00319 ( 20) SS BOND : angle 1.16837 ( 40) covalent geometry : bond 0.00375 ( 9368) covalent geometry : angle 0.62515 (12730) *********************** 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 158 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 1.101 Fit side-chains REVERT: A 3 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8426 (tm-30) REVERT: A 5 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8226 (mm110) REVERT: B 123 GLU cc_start: 0.8402 (mp0) cc_final: 0.8124 (mp0) REVERT: B 142 ARG cc_start: 0.8570 (ttt-90) cc_final: 0.7793 (tmt170) REVERT: B 147 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8714 (mt0) REVERT: G 137 ASP cc_start: 0.7639 (m-30) cc_final: 0.7183 (m-30) REVERT: G 203 PHE cc_start: 0.7765 (t80) cc_final: 0.7475 (t80) REVERT: I 117 MET cc_start: 0.6223 (tmm) cc_final: 0.5597 (mtt) REVERT: I 137 ASP cc_start: 0.7634 (m-30) cc_final: 0.7190 (m-30) REVERT: I 203 PHE cc_start: 0.7734 (t80) cc_final: 0.7448 (t80) REVERT: L 40 CYS cc_start: 0.8221 (m) cc_final: 0.7919 (m) REVERT: L 123 GLU cc_start: 0.8391 (mp0) cc_final: 0.8115 (mp0) REVERT: L 142 ARG cc_start: 0.8572 (ttt-90) cc_final: 0.7809 (tmt170) REVERT: L 147 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8758 (mt0) outliers start: 25 outliers final: 8 residues processed: 148 average time/residue: 1.2978 time to fit residues: 204.7395 Evaluate side-chains 139 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN 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 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 113 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 202 ASN A 204 ASN G 56 GLN H 3 GLN H 5 GLN H 202 ASN H 204 ASN I 56 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.108942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.077892 restraints weight = 16052.839| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.45 r_work: 0.3060 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9388 Z= 0.165 Angle : 0.627 8.763 12770 Z= 0.329 Chirality : 0.043 0.156 1442 Planarity : 0.004 0.047 1594 Dihedral : 4.930 18.114 1280 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.24 % Allowed : 14.98 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 1.31 (0.25), residues: 1190 helix: 1.76 (0.31), residues: 272 sheet: 1.25 (0.24), residues: 428 loop : 0.08 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 89 HIS 0.002 0.001 HIS A 35 PHE 0.014 0.001 PHE H 100D TYR 0.017 0.002 TYR G 86 ARG 0.012 0.001 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 502) hydrogen bonds : angle 4.97335 ( 1410) SS BOND : bond 0.00274 ( 20) SS BOND : angle 1.15434 ( 40) covalent geometry : bond 0.00382 ( 9368) covalent geometry : angle 0.62503 (12730) *********************** 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 155 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.087 Fit side-chains REVERT: B 123 GLU cc_start: 0.8377 (mp0) cc_final: 0.8112 (mp0) REVERT: B 142 ARG cc_start: 0.8616 (ttt-90) cc_final: 0.7760 (tmt170) REVERT: B 147 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8665 (mt0) REVERT: B 167 ASP cc_start: 0.8717 (t0) cc_final: 0.8516 (t0) REVERT: G 117 MET cc_start: 0.6154 (tmm) cc_final: 0.5567 (mtt) REVERT: G 137 ASP cc_start: 0.7630 (m-30) cc_final: 0.7169 (m-30) REVERT: G 203 PHE cc_start: 0.7741 (t80) cc_final: 0.7469 (t80) REVERT: I 117 MET cc_start: 0.6117 (tmm) cc_final: 0.5510 (mtt) REVERT: I 137 ASP cc_start: 0.7623 (m-30) cc_final: 0.7177 (m-30) REVERT: I 203 PHE cc_start: 0.7706 (t80) cc_final: 0.7393 (t80) REVERT: L 123 GLU cc_start: 0.8369 (mp0) cc_final: 0.8100 (mp0) REVERT: L 142 ARG cc_start: 0.8611 (ttt-90) cc_final: 0.7767 (tmt170) REVERT: L 147 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8713 (mt0) outliers start: 23 outliers final: 8 residues processed: 146 average time/residue: 1.3824 time to fit residues: 214.3625 Evaluate side-chains 140 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 1 optimal weight: 0.3980 chunk 110 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 96 optimal weight: 0.0980 chunk 17 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 H 3 GLN H 5 GLN H 202 ASN H 204 ASN ** I 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.107941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.076608 restraints weight = 16178.771| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.46 r_work: 0.3038 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9388 Z= 0.203 Angle : 0.656 8.549 12770 Z= 0.344 Chirality : 0.044 0.150 1442 Planarity : 0.005 0.075 1594 Dihedral : 5.018 18.077 1280 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.24 % Allowed : 15.66 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 1.25 (0.24), residues: 1190 helix: 1.73 (0.31), residues: 270 sheet: 1.21 (0.24), residues: 428 loop : 0.05 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 89 HIS 0.002 0.001 HIS H 169 PHE 0.015 0.002 PHE H 100D TYR 0.018 0.002 TYR G 86 ARG 0.018 0.002 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 502) hydrogen bonds : angle 5.08602 ( 1410) SS BOND : bond 0.00321 ( 20) SS BOND : angle 1.20255 ( 40) covalent geometry : bond 0.00474 ( 9368) covalent geometry : angle 0.65324 (12730) *********************** 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 154 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 1.120 Fit side-chains REVERT: A 3 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8448 (tm-30) REVERT: A 5 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8295 (mm110) REVERT: B 123 GLU cc_start: 0.8432 (mp0) cc_final: 0.8162 (mp0) REVERT: B 142 ARG cc_start: 0.8558 (ttt-90) cc_final: 0.7442 (tpt90) REVERT: B 147 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8696 (mt0) REVERT: G 117 MET cc_start: 0.6219 (tmm) cc_final: 0.5598 (mtt) REVERT: G 137 ASP cc_start: 0.7646 (m-30) cc_final: 0.7207 (m-30) REVERT: G 203 PHE cc_start: 0.7823 (t80) cc_final: 0.7559 (t80) REVERT: H 3 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8474 (tm-30) REVERT: H 5 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8314 (mm110) REVERT: I 117 MET cc_start: 0.6179 (tmm) cc_final: 0.5581 (mtt) REVERT: I 137 ASP cc_start: 0.7658 (m-30) cc_final: 0.7212 (m-30) REVERT: I 203 PHE cc_start: 0.7801 (t80) cc_final: 0.7497 (t80) REVERT: L 123 GLU cc_start: 0.8416 (mp0) cc_final: 0.8144 (mp0) REVERT: L 142 ARG cc_start: 0.8615 (ttt-90) cc_final: 0.7443 (tpt90) REVERT: L 147 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8764 (mt0) outliers start: 23 outliers final: 10 residues processed: 147 average time/residue: 1.5668 time to fit residues: 244.2978 Evaluate side-chains 142 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN 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 55 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.108015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.076086 restraints weight = 15954.877| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.53 r_work: 0.3003 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9388 Z= 0.176 Angle : 0.651 9.012 12770 Z= 0.341 Chirality : 0.044 0.150 1442 Planarity : 0.004 0.055 1594 Dihedral : 4.934 17.914 1280 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.14 % Allowed : 16.05 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 1.30 (0.25), residues: 1190 helix: 1.78 (0.31), residues: 270 sheet: 1.25 (0.24), residues: 428 loop : 0.07 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 89 HIS 0.002 0.001 HIS A 35 PHE 0.014 0.002 PHE H 100D TYR 0.017 0.002 TYR G 86 ARG 0.014 0.002 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 502) hydrogen bonds : angle 5.03300 ( 1410) SS BOND : bond 0.00292 ( 20) SS BOND : angle 1.14404 ( 40) covalent geometry : bond 0.00411 ( 9368) covalent geometry : angle 0.64879 (12730) *********************** 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: 22 poor density : 130 time to evaluate : 1.491 Fit side-chains REVERT: B 123 GLU cc_start: 0.8368 (mp0) cc_final: 0.8097 (mp0) REVERT: B 142 ARG cc_start: 0.8615 (ttt-90) cc_final: 0.7392 (tpt90) REVERT: B 147 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8655 (mt0) REVERT: G 117 MET cc_start: 0.6090 (tmm) cc_final: 0.5516 (mtt) REVERT: G 137 ASP cc_start: 0.7616 (m-30) cc_final: 0.7144 (m-30) REVERT: G 203 PHE cc_start: 0.7686 (t80) cc_final: 0.7393 (t80) REVERT: H 3 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8355 (tm-30) REVERT: H 5 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8203 (mm110) REVERT: I 117 MET cc_start: 0.6055 (tmm) cc_final: 0.5501 (mtt) REVERT: I 137 ASP cc_start: 0.7626 (m-30) cc_final: 0.7140 (m-30) REVERT: I 203 PHE cc_start: 0.7708 (t80) cc_final: 0.7423 (t80) REVERT: L 123 GLU cc_start: 0.8355 (mp0) cc_final: 0.8084 (mp0) REVERT: L 142 ARG cc_start: 0.8621 (ttt-90) cc_final: 0.7394 (tpt90) REVERT: L 147 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8695 (mt0) outliers start: 22 outliers final: 11 residues processed: 145 average time/residue: 1.4550 time to fit residues: 224.3815 Evaluate side-chains 142 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 G residue 206 LEU 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 105 GLU 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 64 optimal weight: 0.4980 chunk 15 optimal weight: 0.3980 chunk 67 optimal weight: 0.9980 chunk 78 optimal weight: 0.0670 chunk 71 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 86 optimal weight: 0.0970 overall best weight: 0.3116 ------------------------------------------------------------------------------- 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 202 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.109859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.078216 restraints weight = 16071.773| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.56 r_work: 0.3048 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9388 Z= 0.129 Angle : 0.638 9.241 12770 Z= 0.332 Chirality : 0.043 0.159 1442 Planarity : 0.004 0.061 1594 Dihedral : 4.734 17.054 1280 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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 (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: 1190 helix: 1.81 (0.31), residues: 272 sheet: 1.32 (0.24), residues: 430 loop : 0.17 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 89 HIS 0.002 0.000 HIS H 35 PHE 0.013 0.001 PHE H 100D TYR 0.016 0.001 TYR G 86 ARG 0.013 0.002 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 502) hydrogen bonds : angle 4.83720 ( 1410) SS BOND : bond 0.00207 ( 20) SS BOND : angle 0.90700 ( 40) covalent geometry : bond 0.00298 ( 9368) covalent geometry : angle 0.63743 (12730) ********************** 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 165 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 ARG cc_start: 0.8553 (ttm110) cc_final: 0.8340 (ttp-110) REVERT: B 123 GLU cc_start: 0.8412 (mp0) cc_final: 0.8155 (mp0) REVERT: B 142 ARG cc_start: 0.8617 (ttt-90) cc_final: 0.7788 (tmt170) REVERT: B 147 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8691 (mt0) REVERT: G 117 MET cc_start: 0.6150 (tmm) cc_final: 0.5602 (mtt) REVERT: G 137 ASP cc_start: 0.7663 (m-30) cc_final: 0.7170 (m-30) REVERT: G 203 PHE cc_start: 0.7693 (t80) cc_final: 0.7420 (t80) REVERT: I 137 ASP cc_start: 0.7679 (m-30) cc_final: 0.7192 (m-30) REVERT: I 203 PHE cc_start: 0.7688 (t80) cc_final: 0.7384 (t80) REVERT: L 123 GLU cc_start: 0.8395 (mp0) cc_final: 0.8134 (mp0) REVERT: L 142 ARG cc_start: 0.8615 (ttt-90) cc_final: 0.7802 (tmt170) REVERT: L 147 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8743 (mt0) outliers start: 19 outliers final: 9 residues processed: 159 average time/residue: 1.4223 time to fit residues: 240.6533 Evaluate side-chains 148 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 33 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.106095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.073852 restraints weight = 16011.219| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.51 r_work: 0.2974 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 9388 Z= 0.270 Angle : 0.713 9.735 12770 Z= 0.371 Chirality : 0.046 0.162 1442 Planarity : 0.005 0.052 1594 Dihedral : 5.078 18.294 1280 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.75 % Allowed : 17.70 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 1.30 (0.25), residues: 1190 helix: 1.61 (0.31), residues: 270 sheet: 1.32 (0.24), residues: 424 loop : 0.12 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 85 HIS 0.002 0.001 HIS H 169 PHE 0.017 0.002 PHE I 62 TYR 0.018 0.002 TYR I 86 ARG 0.013 0.002 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 502) hydrogen bonds : angle 5.19710 ( 1410) SS BOND : bond 0.00417 ( 20) SS BOND : angle 1.31663 ( 40) covalent geometry : bond 0.00633 ( 9368) covalent geometry : angle 0.71006 (12730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9906.46 seconds wall clock time: 175 minutes 15.67 seconds (10515.67 seconds total)