Starting phenix.real_space_refine on Sat Dec 28 22:01:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgo_43216/12_2024/8vgo_43216.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgo_43216/12_2024/8vgo_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_43216/12_2024/8vgo_43216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgo_43216/12_2024/8vgo_43216.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgo_43216/12_2024/8vgo_43216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgo_43216/12_2024/8vgo_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-5532/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: 6.79, per 1000 atoms: 0.74 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: 2.41 Conformation dependent library (CDL) restraints added in 1.2 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: 1.47 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: 2.94 Time building geometry restraints manager: 2.76 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: 0.00 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: 3.250 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.420 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.300 ------------------------------------------------------------------------------- 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 : 1.101 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: 1.4642 time to fit residues: 342.2594 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 : 1.009 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8873 (tt0) cc_final: 0.8650 (tm-30) REVERT: A 152 GLU cc_start: 0.8255 (tt0) cc_final: 0.7887 (tm-30) REVERT: B 147 GLN cc_start: 0.9051 (tp40) cc_final: 0.8798 (mt0) REVERT: G 76 ILE cc_start: 0.7936 (mt) cc_final: 0.7646 (tp) REVERT: G 117 MET cc_start: 0.6038 (tmm) cc_final: 0.5560 (mtt) REVERT: G 137 ASP cc_start: 0.7660 (m-30) cc_final: 0.7080 (m-30) REVERT: G 203 PHE cc_start: 0.7661 (t80) cc_final: 0.7361 (t80) REVERT: H 3 GLN cc_start: 0.8858 (tt0) cc_final: 0.8638 (tm-30) REVERT: H 72 ASP cc_start: 0.8556 (t0) cc_final: 0.8226 (t0) REVERT: H 152 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7731 (tm-30) REVERT: I 76 ILE cc_start: 0.8083 (mt) cc_final: 0.7723 (tp) REVERT: I 85 TRP cc_start: 0.8186 (m100) cc_final: 0.7960 (m100) REVERT: I 117 MET cc_start: 0.6033 (tmm) cc_final: 0.5506 (mtt) REVERT: I 137 ASP cc_start: 0.7661 (m-30) cc_final: 0.7083 (m-30) REVERT: I 203 PHE cc_start: 0.7660 (t80) cc_final: 0.7369 (t80) REVERT: L 147 GLN cc_start: 0.9066 (tp40) cc_final: 0.8827 (mt0) outliers start: 14 outliers final: 4 residues processed: 157 average time/residue: 1.2881 time to fit residues: 215.6172 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 : 1.048 ------------------------------------------------------------------------------- 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 59 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 0.0870 chunk 29 optimal weight: 0.0570 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 86 optimal weight: 0.0570 overall best weight: 0.2194 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9368 Z= 0.149 Angle : 0.578 6.164 12730 Z= 0.306 Chirality : 0.042 0.169 1442 Planarity : 0.004 0.035 1594 Dihedral : 4.968 29.051 1280 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.60 % Favored : 98.24 % Rotamer: Outliers : 1.75 % Allowed : 11.38 % Favored : 86.87 % 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: 1.48 (0.25), residues: 1190 helix: 1.65 (0.32), residues: 280 sheet: 1.31 (0.24), residues: 422 loop : 0.39 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 89 HIS 0.002 0.000 HIS H 35 PHE 0.013 0.001 PHE A 100D TYR 0.022 0.001 TYR G 182 ARG 0.009 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 181 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 1.071 Fit side-chains REVERT: A 3 GLN cc_start: 0.8873 (tt0) cc_final: 0.8629 (tm-30) REVERT: A 215 LYS cc_start: 0.9002 (tttm) cc_final: 0.8785 (tttm) REVERT: B 142 ARG cc_start: 0.8522 (ttt-90) cc_final: 0.7986 (tmt170) REVERT: B 147 GLN cc_start: 0.8999 (tp40) cc_final: 0.8716 (mt0) REVERT: B 170 ASP cc_start: 0.7669 (t0) cc_final: 0.7341 (t0) REVERT: G 46 MET cc_start: 0.4602 (mmm) cc_final: 0.3277 (tmm) REVERT: G 137 ASP cc_start: 0.7677 (m-30) cc_final: 0.7065 (m-30) REVERT: G 203 PHE cc_start: 0.7631 (t80) cc_final: 0.7410 (t80) REVERT: H 3 GLN cc_start: 0.8855 (tt0) cc_final: 0.8581 (tm-30) REVERT: H 72 ASP cc_start: 0.8542 (t0) cc_final: 0.8226 (t0) REVERT: H 152 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7607 (tm-30) REVERT: H 215 LYS cc_start: 0.9017 (tttm) cc_final: 0.8796 (tttm) REVERT: I 46 MET cc_start: 0.4584 (mmm) cc_final: 0.3280 (tmm) REVERT: I 76 ILE cc_start: 0.8057 (mt) cc_final: 0.7784 (tp) REVERT: I 137 ASP cc_start: 0.7700 (m-30) cc_final: 0.7106 (m-30) REVERT: I 203 PHE cc_start: 0.7661 (t80) cc_final: 0.7403 (t80) REVERT: L 142 ARG cc_start: 0.8547 (ttt-90) cc_final: 0.8004 (tmt170) REVERT: L 147 GLN cc_start: 0.9028 (tp40) cc_final: 0.8765 (mt0) REVERT: L 170 ASP cc_start: 0.7688 (t0) cc_final: 0.7327 (t0) outliers start: 18 outliers final: 2 residues processed: 173 average time/residue: 1.2093 time to fit residues: 223.9032 Evaluate side-chains 149 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 LEU 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 106 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 0.0030 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 0.3980 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 102 optimal weight: 0.0770 chunk 30 optimal weight: 1.9990 overall best weight: 0.4748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 204 ASN G 56 GLN H 3 GLN H 60 ASN H 202 ASN H 204 ASN I 56 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2935 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= 0.196 Angle : 0.602 7.260 12730 Z= 0.315 Chirality : 0.043 0.148 1442 Planarity : 0.004 0.059 1594 Dihedral : 4.957 23.844 1280 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.85 % Favored : 97.98 % Rotamer: Outliers : 1.95 % Allowed : 14.20 % 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: 1.47 (0.25), residues: 1190 helix: 1.62 (0.31), residues: 282 sheet: 1.34 (0.24), residues: 422 loop : 0.37 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 89 HIS 0.002 0.001 HIS H 35 PHE 0.015 0.001 PHE H 100D TYR 0.017 0.001 TYR G 86 ARG 0.013 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 169 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8876 (tt0) cc_final: 0.8658 (tt0) REVERT: A 152 GLU cc_start: 0.8126 (tt0) cc_final: 0.7764 (tm-30) REVERT: B 142 ARG cc_start: 0.8643 (ttt-90) cc_final: 0.8029 (tmt170) REVERT: B 147 GLN cc_start: 0.8994 (tp40) cc_final: 0.8710 (mt0) REVERT: G 117 MET cc_start: 0.6186 (tmm) cc_final: 0.5576 (mtt) REVERT: G 137 ASP cc_start: 0.7741 (m-30) cc_final: 0.7311 (m-30) REVERT: G 203 PHE cc_start: 0.7657 (t80) cc_final: 0.7409 (t80) REVERT: H 3 GLN cc_start: 0.8880 (tt0) cc_final: 0.8626 (tt0) REVERT: H 152 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7675 (tm-30) REVERT: I 76 ILE cc_start: 0.8061 (mt) cc_final: 0.7839 (tp) REVERT: I 117 MET cc_start: 0.6158 (tmm) cc_final: 0.5539 (mtt) REVERT: I 137 ASP cc_start: 0.7679 (m-30) cc_final: 0.7245 (m-30) REVERT: I 203 PHE cc_start: 0.7660 (t80) cc_final: 0.7423 (t80) REVERT: L 142 ARG cc_start: 0.8647 (ttt-90) cc_final: 0.8022 (tmt170) REVERT: L 147 GLN cc_start: 0.9043 (tt0) cc_final: 0.8782 (mt0) outliers start: 20 outliers final: 4 residues processed: 159 average time/residue: 1.3630 time to fit residues: 230.5038 Evaluate side-chains 148 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 1.9990 chunk 64 optimal weight: 0.0970 chunk 1 optimal weight: 0.0870 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 28 optimal weight: 0.4980 overall best weight: 0.4556 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3184 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= 0.195 Angle : 0.592 6.299 12730 Z= 0.308 Chirality : 0.042 0.152 1442 Planarity : 0.004 0.041 1594 Dihedral : 4.807 18.533 1280 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.10 % Favored : 97.82 % Rotamer: Outliers : 1.46 % Allowed : 16.05 % 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: 1.52 (0.25), residues: 1190 helix: 1.62 (0.31), residues: 282 sheet: 1.43 (0.24), residues: 422 loop : 0.35 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 89 HIS 0.002 0.001 HIS H 35 PHE 0.014 0.001 PHE H 100D TYR 0.019 0.001 TYR G 182 ARG 0.011 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 162 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8868 (tt0) cc_final: 0.8595 (tt0) REVERT: A 152 GLU cc_start: 0.8070 (tt0) cc_final: 0.7738 (tm-30) REVERT: B 142 ARG cc_start: 0.8644 (ttt-90) cc_final: 0.7944 (tmt170) REVERT: B 147 GLN cc_start: 0.9020 (tp40) cc_final: 0.8732 (mt0) REVERT: G 46 MET cc_start: 0.5122 (mmm) cc_final: 0.3587 (tmm) REVERT: G 76 ILE cc_start: 0.8309 (tp) cc_final: 0.8088 (tp) REVERT: G 137 ASP cc_start: 0.7716 (m-30) cc_final: 0.7278 (m-30) REVERT: G 203 PHE cc_start: 0.7654 (t80) cc_final: 0.7359 (t80) REVERT: H 3 GLN cc_start: 0.8893 (tt0) cc_final: 0.8617 (tm-30) REVERT: H 152 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7868 (tm-30) REVERT: I 46 MET cc_start: 0.5424 (mmm) cc_final: 0.3951 (tmm) REVERT: I 137 ASP cc_start: 0.7747 (m-30) cc_final: 0.7311 (m-30) REVERT: I 203 PHE cc_start: 0.7670 (t80) cc_final: 0.7428 (t80) REVERT: L 142 ARG cc_start: 0.8645 (ttt-90) cc_final: 0.7935 (tmt170) REVERT: L 147 GLN cc_start: 0.9038 (tt0) cc_final: 0.8763 (mt0) outliers start: 15 outliers final: 5 residues processed: 152 average time/residue: 1.3969 time to fit residues: 226.1652 Evaluate side-chains 149 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 144 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain I residue 162 ILE 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 38 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 114 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9368 Z= 0.279 Angle : 0.633 8.688 12730 Z= 0.332 Chirality : 0.044 0.153 1442 Planarity : 0.004 0.066 1594 Dihedral : 4.945 19.057 1280 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.65 % Allowed : 16.05 % Favored : 82.30 % 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: 1.72 (0.31), residues: 272 sheet: 1.37 (0.25), residues: 422 loop : 0.19 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 89 HIS 0.002 0.001 HIS H 169 PHE 0.015 0.002 PHE H 100D TYR 0.017 0.002 TYR I 86 ARG 0.017 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 155 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 1.114 Fit side-chains REVERT: A 3 GLN cc_start: 0.8876 (tt0) cc_final: 0.8669 (tt0) REVERT: A 215 LYS cc_start: 0.9112 (tttm) cc_final: 0.8755 (tttm) REVERT: B 147 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8751 (mt0) REVERT: G 117 MET cc_start: 0.6242 (tmm) cc_final: 0.5668 (mtt) REVERT: G 137 ASP cc_start: 0.7708 (m-30) cc_final: 0.7311 (m-30) REVERT: G 203 PHE cc_start: 0.7793 (t80) cc_final: 0.7522 (t80) REVERT: H 3 GLN cc_start: 0.8910 (tt0) cc_final: 0.8657 (tt0) REVERT: H 152 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7908 (tm-30) REVERT: H 215 LYS cc_start: 0.9109 (tttm) cc_final: 0.8763 (tttm) REVERT: I 117 MET cc_start: 0.6209 (tmm) cc_final: 0.5644 (mtt) REVERT: I 137 ASP cc_start: 0.7705 (m-30) cc_final: 0.7289 (m-30) REVERT: I 203 PHE cc_start: 0.7791 (t80) cc_final: 0.7567 (t80) REVERT: L 147 GLN cc_start: 0.9025 (tt0) cc_final: 0.8743 (mt0) outliers start: 17 outliers final: 4 residues processed: 146 average time/residue: 1.3468 time to fit residues: 209.5095 Evaluate side-chains 141 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 136 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASN 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 L residue 154 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9368 Z= 0.314 Angle : 0.654 8.121 12730 Z= 0.343 Chirality : 0.044 0.155 1442 Planarity : 0.004 0.046 1594 Dihedral : 5.009 18.884 1280 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.85 % Allowed : 16.44 % Favored : 81.71 % 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: 1.65 (0.31), residues: 272 sheet: 1.31 (0.24), residues: 428 loop : 0.20 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 89 HIS 0.002 0.001 HIS H 169 PHE 0.015 0.002 PHE H 100D TYR 0.018 0.002 TYR I 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 152 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 1.081 Fit side-chains REVERT: A 3 GLN cc_start: 0.8897 (tt0) cc_final: 0.8649 (tt0) REVERT: B 142 ARG cc_start: 0.8648 (ttt-90) cc_final: 0.7960 (tmt170) REVERT: B 147 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8729 (mt0) REVERT: G 117 MET cc_start: 0.6238 (tmm) cc_final: 0.5685 (mtt) REVERT: G 137 ASP cc_start: 0.7734 (m-30) cc_final: 0.7306 (m-30) REVERT: G 203 PHE cc_start: 0.7853 (t80) cc_final: 0.7594 (t80) REVERT: H 3 GLN cc_start: 0.8928 (tt0) cc_final: 0.8657 (tt0) REVERT: I 117 MET cc_start: 0.6234 (tmm) cc_final: 0.5660 (mtt) REVERT: I 137 ASP cc_start: 0.7717 (m-30) cc_final: 0.7297 (m-30) REVERT: I 203 PHE cc_start: 0.7847 (t80) cc_final: 0.7550 (t80) REVERT: L 142 ARG cc_start: 0.8656 (ttt-90) cc_final: 0.7952 (tmt170) REVERT: L 147 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8767 (mt0) outliers start: 19 outliers final: 7 residues processed: 142 average time/residue: 1.3987 time to fit residues: 210.8694 Evaluate side-chains 140 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 89 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 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 204 ASN G 56 GLN H 204 ASN ** I 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9368 Z= 0.279 Angle : 0.660 7.562 12730 Z= 0.347 Chirality : 0.044 0.150 1442 Planarity : 0.005 0.076 1594 Dihedral : 4.956 18.707 1280 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.46 % Allowed : 17.12 % Favored : 81.42 % 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: 1.39 (0.25), residues: 1190 helix: 1.71 (0.31), residues: 272 sheet: 1.33 (0.24), residues: 428 loop : 0.19 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 89 HIS 0.002 0.001 HIS H 169 PHE 0.014 0.002 PHE A 100D TYR 0.017 0.002 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 148 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 1.078 Fit side-chains REVERT: A 3 GLN cc_start: 0.8882 (tt0) cc_final: 0.8633 (tt0) REVERT: B 142 ARG cc_start: 0.8659 (ttt-90) cc_final: 0.7965 (tmt170) REVERT: B 147 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8738 (mt0) REVERT: G 117 MET cc_start: 0.6163 (tmm) cc_final: 0.5581 (mtt) REVERT: G 137 ASP cc_start: 0.7738 (m-30) cc_final: 0.7308 (m-30) REVERT: G 203 PHE cc_start: 0.7824 (t80) cc_final: 0.7542 (t80) REVERT: H 3 GLN cc_start: 0.8931 (tt0) cc_final: 0.8653 (tt0) REVERT: I 117 MET cc_start: 0.6176 (tmm) cc_final: 0.5592 (mtt) REVERT: I 137 ASP cc_start: 0.7737 (m-30) cc_final: 0.7303 (m-30) REVERT: I 203 PHE cc_start: 0.7822 (t80) cc_final: 0.7535 (t80) REVERT: L 142 ARG cc_start: 0.8665 (ttt-90) cc_final: 0.7955 (tmt170) REVERT: L 147 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8772 (mt0) outliers start: 15 outliers final: 7 residues processed: 141 average time/residue: 1.3687 time to fit residues: 205.3847 Evaluate side-chains 138 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASN 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 69 optimal weight: 0.3980 chunk 112 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 204 ASN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 ASN ** I 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3430 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= 0.261 Angle : 0.660 7.338 12730 Z= 0.345 Chirality : 0.044 0.149 1442 Planarity : 0.004 0.055 1594 Dihedral : 4.876 18.572 1280 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.95 % Allowed : 16.73 % Favored : 81.32 % 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: 1.43 (0.25), residues: 1190 helix: 1.74 (0.31), residues: 272 sheet: 1.35 (0.24), residues: 428 loop : 0.22 (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 0.014 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 152 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 1.016 Fit side-chains REVERT: A 3 GLN cc_start: 0.8889 (tt0) cc_final: 0.8641 (tt0) REVERT: B 142 ARG cc_start: 0.8661 (ttt-90) cc_final: 0.7959 (tmt170) REVERT: B 147 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8707 (mt0) REVERT: G 117 MET cc_start: 0.6149 (tmm) cc_final: 0.5573 (mtt) REVERT: G 137 ASP cc_start: 0.7758 (m-30) cc_final: 0.7322 (m-30) REVERT: G 203 PHE cc_start: 0.7827 (t80) cc_final: 0.7558 (t80) REVERT: H 3 GLN cc_start: 0.8928 (tt0) cc_final: 0.8647 (tt0) REVERT: I 117 MET cc_start: 0.6161 (tmm) cc_final: 0.5591 (mtt) REVERT: I 137 ASP cc_start: 0.7746 (m-30) cc_final: 0.7321 (m-30) REVERT: I 203 PHE cc_start: 0.7839 (t80) cc_final: 0.7537 (t80) REVERT: L 142 ARG cc_start: 0.8668 (ttt-90) cc_final: 0.7936 (tmt170) REVERT: L 147 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8773 (mt0) outliers start: 20 outliers final: 8 residues processed: 145 average time/residue: 1.3972 time to fit residues: 216.1414 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 : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASN 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 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 68 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 ASN ** I 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9368 Z= 0.288 Angle : 0.682 8.440 12730 Z= 0.356 Chirality : 0.044 0.153 1442 Planarity : 0.005 0.083 1594 Dihedral : 4.918 18.726 1280 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.56 % Allowed : 17.32 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.40 (0.25), residues: 1190 helix: 1.67 (0.31), residues: 272 sheet: 1.35 (0.24), residues: 428 loop : 0.20 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 89 HIS 0.002 0.001 HIS A 169 PHE 0.014 0.002 PHE A 100D TYR 0.017 0.002 TYR G 86 ARG 0.019 0.002 ARG B 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 148 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.976 Fit side-chains REVERT: A 3 GLN cc_start: 0.8888 (tt0) cc_final: 0.8637 (tt0) REVERT: B 142 ARG cc_start: 0.8666 (ttt-90) cc_final: 0.7940 (tmt170) REVERT: B 147 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8706 (mt0) REVERT: G 117 MET cc_start: 0.6143 (tmm) cc_final: 0.5625 (mtt) REVERT: G 137 ASP cc_start: 0.7761 (m-30) cc_final: 0.7325 (m-30) REVERT: G 203 PHE cc_start: 0.7817 (t80) cc_final: 0.7547 (t80) REVERT: H 3 GLN cc_start: 0.8926 (tt0) cc_final: 0.8681 (tt0) REVERT: I 117 MET cc_start: 0.6202 (tmm) cc_final: 0.5600 (mtt) REVERT: I 137 ASP cc_start: 0.7747 (m-30) cc_final: 0.7320 (m-30) REVERT: I 203 PHE cc_start: 0.7869 (t80) cc_final: 0.7568 (t80) REVERT: L 142 ARG cc_start: 0.8677 (ttt-90) cc_final: 0.7927 (tmt170) REVERT: L 147 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8777 (mt0) outliers start: 16 outliers final: 9 residues processed: 142 average time/residue: 1.3648 time to fit residues: 206.1012 Evaluate side-chains 140 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASN 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 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 28 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 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 204 ASN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 ASN ** I 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.109072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.077799 restraints weight = 15828.958| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.45 r_work: 0.3068 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9368 Z= 0.268 Angle : 0.676 9.118 12730 Z= 0.352 Chirality : 0.044 0.150 1442 Planarity : 0.004 0.055 1594 Dihedral : 4.852 18.605 1280 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.46 % Allowed : 17.80 % 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: 1.41 (0.25), residues: 1190 helix: 1.64 (0.31), residues: 272 sheet: 1.38 (0.24), residues: 428 loop : 0.20 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 89 HIS 0.001 0.001 HIS H 169 PHE 0.014 0.002 PHE H 100D TYR 0.017 0.002 TYR G 86 ARG 0.014 0.002 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4237.66 seconds wall clock time: 76 minutes 44.15 seconds (4604.15 seconds total)