Starting phenix.real_space_refine on Thu Jan 16 07:07:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgo_43216/01_2025/8vgo_43216.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgo_43216/01_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_43216/01_2025/8vgo_43216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgo_43216/01_2025/8vgo_43216.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgo_43216/01_2025/8vgo_43216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgo_43216/01_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-5571/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: 6.56, 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: 2.38 Conformation dependent library (CDL) restraints added in 1.1 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: 1.50 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: 3.03 Time building geometry restraints manager: 2.70 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: 0.01 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: 0.010 Normalize map: mean=0, sd=1: 4.930 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.510 Find NCS groups from input model: 0.260 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:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.160 ------------------------------------------------------------------------------- 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 9368 Z= 0.201 Angle : 0.676 6.503 12730 Z= 0.374 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 *********************** 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 : 1.012 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: 1.4618 time to fit residues: 341.7578 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 : 0.979 ------------------------------------------------------------------------------- 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 = 0.106624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.073746 restraints weight = 15022.879| |-----------------------------------------------------------------------------| 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: 0.2736 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- 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 9368 Z= 0.211 Angle : 0.646 6.604 12730 Z= 0.344 Chirality : 0.044 0.151 1442 Planarity : 0.005 0.051 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 *********************** 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 : 0.990 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: 0.8225 (tt0) cc_final: 0.7877 (tm-30) REVERT: B 123 GLU cc_start: 0.8342 (mp0) cc_final: 0.8128 (mp0) REVERT: B 147 GLN cc_start: 0.9072 (tp40) cc_final: 0.8825 (mt0) REVERT: B 187 GLU cc_start: 0.9245 (mt-10) cc_final: 0.9041 (mm-30) REVERT: G 76 ILE cc_start: 0.7961 (mt) cc_final: 0.7680 (tp) REVERT: G 117 MET cc_start: 0.6021 (tmm) cc_final: 0.5544 (mtt) REVERT: G 137 ASP cc_start: 0.7671 (m-30) cc_final: 0.7066 (m-30) REVERT: G 203 PHE cc_start: 0.7682 (t80) cc_final: 0.7385 (t80) REVERT: H 3 GLN cc_start: 0.8793 (tt0) cc_final: 0.8575 (tm-30) REVERT: H 72 ASP cc_start: 0.8564 (t0) cc_final: 0.8230 (t0) REVERT: H 152 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7669 (tm-30) REVERT: I 76 ILE cc_start: 0.8114 (mt) cc_final: 0.7767 (tp) REVERT: I 85 TRP cc_start: 0.8209 (m100) cc_final: 0.7980 (m100) REVERT: I 117 MET cc_start: 0.6007 (tmm) cc_final: 0.5478 (mtt) REVERT: I 137 ASP cc_start: 0.7668 (m-30) cc_final: 0.7072 (m-30) REVERT: I 203 PHE cc_start: 0.7678 (t80) cc_final: 0.7392 (t80) REVERT: L 123 GLU cc_start: 0.8337 (mp0) cc_final: 0.8133 (mp0) REVERT: L 147 GLN cc_start: 0.9083 (tp40) cc_final: 0.8849 (mt0) REVERT: L 187 GLU cc_start: 0.9240 (mt-10) cc_final: 0.9032 (mm-30) outliers start: 14 outliers final: 4 residues processed: 157 average time/residue: 1.3184 time to fit residues: 220.4627 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 : 0.982 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.6980 chunk 73 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 56 GLN I 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.102117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.068134 restraints weight = 15321.743| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.54 r_work: 0.2783 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 9368 Z= 0.366 Angle : 0.657 6.102 12730 Z= 0.349 Chirality : 0.046 0.194 1442 Planarity : 0.004 0.039 1594 Dihedral : 5.549 36.044 1280 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.93 % Favored : 97.90 % Rotamer: Outliers : 1.95 % Allowed : 11.48 % Favored : 86.58 % 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: 1.01 (0.24), residues: 1190 helix: 1.22 (0.31), residues: 280 sheet: 1.09 (0.24), residues: 422 loop : 0.07 (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 G 182 ARG 0.008 0.001 ARG L 142 *********************** 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 170 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.8204 (tt0) cc_final: 0.7886 (tm-30) REVERT: B 123 GLU cc_start: 0.8327 (mp0) cc_final: 0.8073 (mp0) REVERT: B 142 ARG cc_start: 0.8620 (ttt-90) cc_final: 0.7818 (tmt170) REVERT: B 147 GLN cc_start: 0.9037 (tp40) cc_final: 0.8764 (mt0) REVERT: B 170 ASP cc_start: 0.7988 (t0) cc_final: 0.7602 (t0) REVERT: G 76 ILE cc_start: 0.8134 (mt) cc_final: 0.7899 (tp) REVERT: G 137 ASP cc_start: 0.7604 (m-30) cc_final: 0.7170 (m-30) REVERT: G 203 PHE cc_start: 0.7827 (t80) cc_final: 0.7559 (t80) REVERT: H 152 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7751 (tm-30) REVERT: I 76 ILE cc_start: 0.8131 (mt) cc_final: 0.7888 (tp) REVERT: I 85 TRP cc_start: 0.8342 (m100) cc_final: 0.8119 (m100) REVERT: I 137 ASP cc_start: 0.7634 (m-30) cc_final: 0.7224 (m-30) REVERT: I 203 PHE cc_start: 0.7835 (t80) cc_final: 0.7562 (t80) REVERT: L 123 GLU cc_start: 0.8325 (mp0) cc_final: 0.8074 (mp0) REVERT: L 142 ARG cc_start: 0.8628 (ttt-90) cc_final: 0.7818 (tmt170) REVERT: L 147 GLN cc_start: 0.9104 (tp40) cc_final: 0.8864 (mt0) REVERT: L 170 ASP cc_start: 0.8002 (t0) cc_final: 0.7627 (t0) outliers start: 20 outliers final: 3 residues processed: 159 average time/residue: 1.3042 time to fit residues: 221.0070 Evaluate side-chains 146 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 LEU 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: 0.7980 chunk 66 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 27 optimal weight: 0.2980 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.104057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.070488 restraints weight = 14774.983| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.49 r_work: 0.2795 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9368 Z= 0.234 Angle : 0.615 7.910 12730 Z= 0.324 Chirality : 0.043 0.166 1442 Planarity : 0.004 0.055 1594 Dihedral : 5.204 30.049 1280 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.24 % Allowed : 13.42 % Favored : 84.34 % 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: 1.41 (0.31), residues: 282 sheet: 1.15 (0.24), residues: 422 loop : 0.10 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 89 HIS 0.003 0.001 HIS H 35 PHE 0.015 0.002 PHE H 100D TYR 0.017 0.002 TYR I 86 ARG 0.014 0.001 ARG B 24 *********************** 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 172 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.988 Fit side-chains REVERT: A 5 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8200 (tp40) REVERT: A 152 GLU cc_start: 0.8065 (tt0) cc_final: 0.7716 (tm-30) REVERT: B 123 GLU cc_start: 0.8236 (mp0) cc_final: 0.7971 (mp0) REVERT: B 142 ARG cc_start: 0.8604 (ttt-90) cc_final: 0.7745 (tmt170) REVERT: B 147 GLN cc_start: 0.8981 (tp40) cc_final: 0.8710 (mt0) REVERT: B 183 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7767 (tttm) REVERT: G 117 MET cc_start: 0.5994 (tmm) cc_final: 0.5484 (mtt) REVERT: G 137 ASP cc_start: 0.7598 (m-30) cc_final: 0.6960 (m-30) REVERT: G 203 PHE cc_start: 0.7626 (t80) cc_final: 0.7333 (t80) REVERT: H 152 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7704 (tm-30) REVERT: I 76 ILE cc_start: 0.7955 (mt) cc_final: 0.7713 (tp) REVERT: I 117 MET cc_start: 0.6021 (tmm) cc_final: 0.5425 (mtt) REVERT: I 137 ASP cc_start: 0.7566 (m-30) cc_final: 0.6958 (m-30) REVERT: I 203 PHE cc_start: 0.7595 (t80) cc_final: 0.7299 (t80) REVERT: L 123 GLU cc_start: 0.8241 (mp0) cc_final: 0.7970 (mp0) REVERT: L 142 ARG cc_start: 0.8601 (ttt-90) cc_final: 0.7679 (tmt170) REVERT: L 147 GLN cc_start: 0.8970 (tt0) cc_final: 0.8729 (mt0) REVERT: L 183 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7767 (tttm) outliers start: 23 outliers final: 4 residues processed: 163 average time/residue: 1.3718 time to fit residues: 237.7276 Evaluate side-chains 142 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 136 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain I residue 51 THR 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: 0.9980 chunk 78 optimal weight: 0.0010 chunk 82 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 61 optimal weight: 0.5980 chunk 96 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 overall best weight: 0.4186 ------------------------------------------------------------------------------- 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 204 ASN I 56 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.107337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.074702 restraints weight = 15039.862| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.48 r_work: 0.2942 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9368 Z= 0.195 Angle : 0.595 6.320 12730 Z= 0.314 Chirality : 0.042 0.152 1442 Planarity : 0.004 0.043 1594 Dihedral : 4.999 24.263 1280 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.85 % Allowed : 14.11 % Favored : 84.05 % 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: 1.34 (0.25), residues: 1190 helix: 1.78 (0.31), residues: 272 sheet: 1.29 (0.24), residues: 422 loop : 0.11 (0.30), residues: 496 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 G 62 TYR 0.020 0.002 TYR G 182 ARG 0.010 0.001 ARG L 24 *********************** 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: 19 poor density : 146 time to evaluate : 1.070 Fit side-chains REVERT: A 3 GLN cc_start: 0.8810 (tt0) cc_final: 0.8604 (tm-30) REVERT: A 152 GLU cc_start: 0.8022 (tt0) cc_final: 0.7757 (tm-30) REVERT: B 40 CYS cc_start: 0.8087 (m) cc_final: 0.7782 (m) REVERT: B 123 GLU cc_start: 0.8398 (mp0) cc_final: 0.8125 (mp0) REVERT: B 142 ARG cc_start: 0.8624 (ttt-90) cc_final: 0.7882 (tmt170) REVERT: B 147 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8786 (mt0) REVERT: G 137 ASP cc_start: 0.7717 (m-30) cc_final: 0.7258 (m-30) REVERT: G 203 PHE cc_start: 0.7721 (t80) cc_final: 0.7425 (t80) REVERT: H 5 GLN cc_start: 0.8750 (mm110) cc_final: 0.8531 (mm110) REVERT: H 152 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7828 (tm-30) REVERT: I 137 ASP cc_start: 0.7698 (m-30) cc_final: 0.7257 (m-30) REVERT: I 203 PHE cc_start: 0.7728 (t80) cc_final: 0.7492 (t80) REVERT: L 123 GLU cc_start: 0.8393 (mp0) cc_final: 0.8122 (mp0) REVERT: L 142 ARG cc_start: 0.8654 (ttt-90) cc_final: 0.7933 (tmt170) REVERT: L 147 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8830 (mt0) outliers start: 19 outliers final: 2 residues processed: 156 average time/residue: 1.4168 time to fit residues: 235.1736 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 : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 154 LEU 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: 0.8980 chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 101 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.106601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.074470 restraints weight = 14803.858| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.35 r_work: 0.2916 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9368 Z= 0.273 Angle : 0.628 8.573 12730 Z= 0.330 Chirality : 0.044 0.156 1442 Planarity : 0.004 0.067 1594 Dihedral : 5.030 19.560 1280 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.53 % Allowed : 14.59 % 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: 1.30 (0.24), residues: 1190 helix: 1.73 (0.31), residues: 272 sheet: 1.23 (0.24), residues: 428 loop : 0.11 (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 0.002 PHE H 100D TYR 0.017 0.002 TYR G 86 ARG 0.016 0.001 ARG B 24 *********************** 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 157 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.079 Fit side-chains REVERT: A 20 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.9218 (ptp) REVERT: B 123 GLU cc_start: 0.8472 (mp0) cc_final: 0.8210 (mp0) REVERT: B 147 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8802 (mt0) REVERT: G 117 MET cc_start: 0.6342 (tmm) cc_final: 0.5732 (mtt) REVERT: G 137 ASP cc_start: 0.7694 (m-30) cc_final: 0.7266 (m-30) REVERT: G 203 PHE cc_start: 0.7918 (t80) cc_final: 0.7651 (t80) REVERT: H 3 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8594 (tm-30) REVERT: I 117 MET cc_start: 0.6336 (tmm) cc_final: 0.5714 (mtt) REVERT: I 137 ASP cc_start: 0.7711 (m-30) cc_final: 0.7326 (m-30) REVERT: I 203 PHE cc_start: 0.7921 (t80) cc_final: 0.7627 (t80) REVERT: L 40 CYS cc_start: 0.8090 (m) cc_final: 0.7779 (m) REVERT: L 123 GLU cc_start: 0.8476 (mp0) cc_final: 0.8213 (mp0) REVERT: L 147 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8847 (mt0) outliers start: 26 outliers final: 6 residues processed: 147 average time/residue: 1.4382 time to fit residues: 224.6361 Evaluate side-chains 142 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 CYS Chi-restraints excluded: chain A residue 20 MET 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 113 optimal weight: 0.3980 chunk 50 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 15 optimal weight: 0.0870 chunk 69 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 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 = 0.3638 r_free = 0.3638 target = 0.109249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.078260 restraints weight = 16074.522| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.45 r_work: 0.3068 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9368 Z= 0.223 Angle : 0.620 7.932 12730 Z= 0.324 Chirality : 0.043 0.151 1442 Planarity : 0.004 0.047 1594 Dihedral : 4.883 18.122 1280 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.85 % Allowed : 15.66 % Favored : 82.49 % 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: 1.38 (0.25), residues: 1190 helix: 1.80 (0.31), residues: 272 sheet: 1.30 (0.24), residues: 428 loop : 0.14 (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 205 PHE 0.013 0.001 PHE H 100D TYR 0.016 0.001 TYR G 86 ARG 0.012 0.001 ARG L 24 *********************** 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 154 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.985 Fit side-chains REVERT: A 20 MET cc_start: 0.9455 (OUTLIER) cc_final: 0.9208 (ptp) REVERT: B 123 GLU cc_start: 0.8407 (mp0) cc_final: 0.8140 (mp0) REVERT: B 142 ARG cc_start: 0.8615 (ttt-90) cc_final: 0.7884 (tmt170) REVERT: B 147 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8692 (mt0) REVERT: G 117 MET cc_start: 0.6209 (tmm) cc_final: 0.5596 (mtt) REVERT: G 137 ASP cc_start: 0.7643 (m-30) cc_final: 0.7188 (m-30) REVERT: G 203 PHE cc_start: 0.7752 (t80) cc_final: 0.7485 (t80) REVERT: I 117 MET cc_start: 0.6168 (tmm) cc_final: 0.5561 (mtt) REVERT: I 137 ASP cc_start: 0.7672 (m-30) cc_final: 0.7225 (m-30) REVERT: I 203 PHE cc_start: 0.7715 (t80) cc_final: 0.7442 (t80) REVERT: L 123 GLU cc_start: 0.8394 (mp0) cc_final: 0.8126 (mp0) REVERT: L 142 ARG cc_start: 0.8601 (ttt-90) cc_final: 0.7877 (tmt170) REVERT: L 147 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8757 (mt0) outliers start: 19 outliers final: 8 residues processed: 146 average time/residue: 1.3838 time to fit residues: 214.8826 Evaluate side-chains 141 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 CYS Chi-restraints excluded: chain A residue 20 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 1 optimal weight: 0.4980 chunk 110 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 88 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 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 204 ASN G 56 GLN H 3 GLN H 5 GLN 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 = 0.3631 r_free = 0.3631 target = 0.108741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.077581 restraints weight = 16199.896| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.46 r_work: 0.3066 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9368 Z= 0.255 Angle : 0.637 7.489 12730 Z= 0.334 Chirality : 0.043 0.158 1442 Planarity : 0.005 0.075 1594 Dihedral : 4.902 17.891 1280 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.14 % Allowed : 15.66 % Favored : 82.20 % 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: 1.37 (0.25), residues: 1190 helix: 1.81 (0.31), residues: 270 sheet: 1.29 (0.24), residues: 428 loop : 0.12 (0.30), residues: 492 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 0.001 TYR G 86 ARG 0.018 0.002 ARG B 24 *********************** 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 156 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 1.107 Fit side-chains REVERT: A 20 MET cc_start: 0.9464 (OUTLIER) cc_final: 0.9214 (ptp) REVERT: B 123 GLU cc_start: 0.8446 (mp0) cc_final: 0.8184 (mp0) REVERT: B 142 ARG cc_start: 0.8594 (ttt-90) cc_final: 0.7881 (tmt170) REVERT: B 147 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8716 (mt0) REVERT: G 117 MET cc_start: 0.6216 (tmm) cc_final: 0.5606 (mtt) REVERT: G 137 ASP cc_start: 0.7678 (m-30) cc_final: 0.7229 (m-30) REVERT: G 203 PHE cc_start: 0.7851 (t80) cc_final: 0.7579 (t80) REVERT: H 3 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8588 (tm-30) REVERT: H 5 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8311 (mm110) REVERT: I 117 MET cc_start: 0.6217 (tmm) cc_final: 0.5627 (mtt) REVERT: I 137 ASP cc_start: 0.7699 (m-30) cc_final: 0.7276 (m-30) REVERT: I 203 PHE cc_start: 0.7794 (t80) cc_final: 0.7521 (t80) REVERT: L 123 GLU cc_start: 0.8433 (mp0) cc_final: 0.8169 (mp0) REVERT: L 142 ARG cc_start: 0.8604 (ttt-90) cc_final: 0.7912 (tmt170) REVERT: L 147 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8766 (mt0) outliers start: 22 outliers final: 11 residues processed: 150 average time/residue: 1.3812 time to fit residues: 220.5128 Evaluate side-chains 146 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 CYS Chi-restraints excluded: chain A residue 20 MET 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 51 THR 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: 3.9990 chunk 48 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 11 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ** 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 = 0.3641 r_free = 0.3641 target = 0.109468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.078181 restraints weight = 15894.462| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.47 r_work: 0.3052 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9368 Z= 0.244 Angle : 0.641 9.132 12730 Z= 0.335 Chirality : 0.043 0.159 1442 Planarity : 0.004 0.055 1594 Dihedral : 4.846 17.742 1280 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.95 % Allowed : 16.25 % 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: 1.41 (0.25), residues: 1190 helix: 1.82 (0.31), residues: 270 sheet: 1.34 (0.24), residues: 428 loop : 0.13 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 89 HIS 0.001 0.001 HIS A 205 PHE 0.014 0.001 PHE H 100D TYR 0.016 0.001 TYR G 86 ARG 0.014 0.001 ARG L 24 *********************** 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 157 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.878 Fit side-chains REVERT: A 20 MET cc_start: 0.9451 (OUTLIER) cc_final: 0.9188 (ptp) REVERT: B 123 GLU cc_start: 0.8397 (mp0) cc_final: 0.8133 (mp0) REVERT: B 142 ARG cc_start: 0.8609 (ttt-90) cc_final: 0.7814 (tmt170) REVERT: B 147 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8678 (mt0) REVERT: G 137 ASP cc_start: 0.7608 (m-30) cc_final: 0.7154 (m-30) REVERT: G 203 PHE cc_start: 0.7750 (t80) cc_final: 0.7445 (t80) REVERT: H 3 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8453 (tm-30) REVERT: H 5 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8193 (mm110) REVERT: I 117 MET cc_start: 0.6176 (tmm) cc_final: 0.5574 (mtt) REVERT: I 137 ASP cc_start: 0.7639 (m-30) cc_final: 0.7189 (m-30) REVERT: I 203 PHE cc_start: 0.7717 (t80) cc_final: 0.7421 (t80) REVERT: L 123 GLU cc_start: 0.8384 (mp0) cc_final: 0.8121 (mp0) REVERT: L 142 ARG cc_start: 0.8577 (ttt-90) cc_final: 0.7820 (tmt170) REVERT: L 147 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8738 (mt0) outliers start: 20 outliers final: 10 residues processed: 151 average time/residue: 1.3908 time to fit residues: 223.0050 Evaluate side-chains 146 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 CYS Chi-restraints excluded: chain A residue 20 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 64 optimal weight: 0.0270 chunk 15 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 0.0370 chunk 71 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 61 GLN A 202 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.109942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.078627 restraints weight = 16008.344| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.48 r_work: 0.3097 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9368 Z= 0.225 Angle : 0.649 9.142 12730 Z= 0.338 Chirality : 0.043 0.159 1442 Planarity : 0.005 0.060 1594 Dihedral : 4.805 17.438 1280 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.85 % Allowed : 17.12 % Favored : 81.03 % 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: 1.46 (0.25), residues: 1190 helix: 1.84 (0.31), residues: 270 sheet: 1.37 (0.24), residues: 428 loop : 0.18 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 89 HIS 0.002 0.000 HIS A 205 PHE 0.014 0.001 PHE H 100D TYR 0.016 0.001 TYR G 86 ARG 0.014 0.002 ARG L 24 ********************** 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 158 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 1.129 Fit side-chains REVERT: A 3 GLN cc_start: 0.8744 (tt0) cc_final: 0.8492 (tm-30) REVERT: A 5 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8268 (mm110) REVERT: A 20 MET cc_start: 0.9456 (OUTLIER) cc_final: 0.9233 (ptp) REVERT: B 123 GLU cc_start: 0.8445 (mp0) cc_final: 0.8183 (mp0) REVERT: B 142 ARG cc_start: 0.8655 (ttt-90) cc_final: 0.7872 (tmt170) REVERT: B 147 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8724 (mt0) REVERT: G 117 MET cc_start: 0.6374 (tmm) cc_final: 0.5704 (mtt) REVERT: G 137 ASP cc_start: 0.7668 (m-30) cc_final: 0.7211 (m-30) REVERT: G 203 PHE cc_start: 0.7762 (t80) cc_final: 0.7483 (t80) REVERT: H 3 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8430 (tm-30) REVERT: H 5 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8228 (mm110) REVERT: I 117 MET cc_start: 0.6339 (tmm) cc_final: 0.5711 (mtt) REVERT: I 137 ASP cc_start: 0.7674 (m-30) cc_final: 0.7218 (m-30) REVERT: I 203 PHE cc_start: 0.7750 (t80) cc_final: 0.7461 (t80) REVERT: L 123 GLU cc_start: 0.8409 (mp0) cc_final: 0.8152 (mp0) REVERT: L 142 ARG cc_start: 0.8649 (ttt-90) cc_final: 0.7891 (tmt170) REVERT: L 147 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8710 (mt0) outliers start: 19 outliers final: 10 residues processed: 152 average time/residue: 1.4021 time to fit residues: 226.6579 Evaluate side-chains 147 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 CYS Chi-restraints excluded: chain A residue 20 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.106130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.073908 restraints weight = 15996.722| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.51 r_work: 0.2963 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 9368 Z= 0.380 Angle : 0.706 8.848 12730 Z= 0.368 Chirality : 0.046 0.160 1442 Planarity : 0.005 0.054 1594 Dihedral : 5.097 18.386 1280 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.04 % Allowed : 17.22 % Favored : 80.74 % 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: 1.59 (0.31), residues: 270 sheet: 1.34 (0.24), residues: 422 loop : 0.10 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 85 HIS 0.002 0.001 HIS A 169 PHE 0.018 0.002 PHE G 62 TYR 0.018 0.002 TYR G 86 ARG 0.014 0.002 ARG B 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8679.66 seconds wall clock time: 155 minutes 15.38 seconds (9315.38 seconds total)