Starting phenix.real_space_refine on Sat Aug 3 06:52:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi3_43247/08_2024/8vi3_43247.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi3_43247/08_2024/8vi3_43247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi3_43247/08_2024/8vi3_43247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi3_43247/08_2024/8vi3_43247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi3_43247/08_2024/8vi3_43247.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi3_43247/08_2024/8vi3_43247.cif" } resolution = 2.9 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= -0.001 sd= 0.017 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 27 5.16 5 C 4988 2.51 5 N 1140 2.21 5 O 1204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7359 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2455 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 308, 2452 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 13, 'TRANS': 294} Conformer: "B" Number of residues, atoms: 308, 2452 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 13, 'TRANS': 294} bond proxies already assigned to first conformer: 2529 Chain: "B" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2452 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 13, 'TRANS': 294} Chain: "C" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2452 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 13, 'TRANS': 294} Time building chain proxies: 7.41, per 1000 atoms: 1.01 Number of scatterers: 7359 At special positions: 0 Unit cell: (97.352, 98.484, 62.26, 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 27 16.00 O 1204 8.00 N 1140 7.00 C 4988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 2.0 seconds 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 90.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 10 through 13 Processing helix chain 'A' and resid 14 through 29 Processing helix chain 'A' and resid 36 through 66 Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 78 through 83 removed outlier: 3.636A pdb=" N SER A 81 " --> pdb=" O VAL A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 98 Processing helix chain 'A' and resid 101 through 124 Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.585A pdb=" N THR A 138 " --> pdb=" O GLN A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 142 through 147 removed outlier: 3.821A pdb=" N ALA A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 161 Processing helix chain 'A' and resid 162 through 192 Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 194 through 199 removed outlier: 4.263A pdb=" N ALA A 199 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 205 through 219 removed outlier: 3.946A pdb=" N PHE A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 249 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 254 through 257 Processing helix chain 'A' and resid 258 through 277 removed outlier: 4.060A pdb=" N PHE A 262 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 309 Processing helix chain 'B' and resid 10 through 13 Processing helix chain 'B' and resid 14 through 29 Processing helix chain 'B' and resid 36 through 66 Processing helix chain 'B' and resid 66 through 76 Processing helix chain 'B' and resid 78 through 83 removed outlier: 3.526A pdb=" N SER B 81 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 98 Processing helix chain 'B' and resid 101 through 124 Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.651A pdb=" N THR B 138 " --> pdb=" O GLN B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 142 through 147 removed outlier: 3.769A pdb=" N ALA B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 161 Processing helix chain 'B' and resid 162 through 192 Proline residue: B 182 - end of helix Processing helix chain 'B' and resid 194 through 199 removed outlier: 4.310A pdb=" N ALA B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 205 through 219 removed outlier: 3.948A pdb=" N PHE B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 249 Proline residue: B 246 - end of helix Processing helix chain 'B' and resid 254 through 257 Processing helix chain 'B' and resid 258 through 277 removed outlier: 4.025A pdb=" N PHE B 262 " --> pdb=" O TRP B 258 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 309 Processing helix chain 'C' and resid 10 through 13 Processing helix chain 'C' and resid 14 through 29 Processing helix chain 'C' and resid 36 through 66 Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 78 through 83 removed outlier: 3.620A pdb=" N SER C 81 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 98 Processing helix chain 'C' and resid 101 through 124 Processing helix chain 'C' and resid 125 through 130 Processing helix chain 'C' and resid 134 through 138 removed outlier: 3.677A pdb=" N THR C 138 " --> pdb=" O GLN C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 142 through 147 removed outlier: 3.745A pdb=" N ALA C 146 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 161 Processing helix chain 'C' and resid 162 through 191 Proline residue: C 182 - end of helix Processing helix chain 'C' and resid 194 through 199 removed outlier: 4.332A pdb=" N ALA C 199 " --> pdb=" O PRO C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 205 through 219 removed outlier: 3.954A pdb=" N PHE C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 249 Proline residue: C 246 - end of helix Processing helix chain 'C' and resid 254 through 257 Processing helix chain 'C' and resid 258 through 277 removed outlier: 4.078A pdb=" N PHE C 262 " --> pdb=" O TRP C 258 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY C 263 " --> pdb=" O ALA C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 309 575 hydrogen bonds defined for protein. 1634 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: 2.26 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2154 1.34 - 1.46: 1884 1.46 - 1.58: 3514 1.58 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 7603 Sorted by residual: bond pdb=" N VAL B 223 " pdb=" CA VAL B 223 " ideal model delta sigma weight residual 1.474 1.458 0.017 1.57e-02 4.06e+03 1.12e+00 bond pdb=" CA VAL A 223 " pdb=" CB VAL A 223 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 9.72e-01 bond pdb=" CB TRP B 231 " pdb=" CG TRP B 231 " ideal model delta sigma weight residual 1.498 1.471 0.027 3.10e-02 1.04e+03 7.75e-01 bond pdb=" CB GLU C 68 " pdb=" CG GLU C 68 " ideal model delta sigma weight residual 1.520 1.539 -0.019 3.00e-02 1.11e+03 4.09e-01 bond pdb=" C ILE A 229 " pdb=" O ILE A 229 " ideal model delta sigma weight residual 1.237 1.244 -0.007 1.17e-02 7.31e+03 3.46e-01 ... (remaining 7598 not shown) Histogram of bond angle deviations from ideal: 100.49 - 107.19: 252 107.19 - 113.88: 4174 113.88 - 120.58: 3373 120.58 - 127.28: 2456 127.28 - 133.97: 117 Bond angle restraints: 10372 Sorted by residual: angle pdb=" N PHE B 7 " pdb=" CA PHE B 7 " pdb=" C PHE B 7 " ideal model delta sigma weight residual 109.72 113.77 -4.05 1.25e+00 6.40e-01 1.05e+01 angle pdb=" N VAL B 223 " pdb=" CA VAL B 223 " pdb=" C VAL B 223 " ideal model delta sigma weight residual 106.21 109.20 -2.99 1.07e+00 8.73e-01 7.79e+00 angle pdb=" N TRP B 231 " pdb=" CA TRP B 231 " pdb=" CB TRP B 231 " ideal model delta sigma weight residual 110.12 113.56 -3.44 1.47e+00 4.63e-01 5.48e+00 angle pdb=" CA VAL B 223 " pdb=" C VAL B 223 " pdb=" O VAL B 223 " ideal model delta sigma weight residual 122.63 120.86 1.77 8.70e-01 1.32e+00 4.13e+00 angle pdb=" N PHE B 7 " pdb=" CA PHE B 7 " pdb=" CB PHE B 7 " ideal model delta sigma weight residual 110.32 113.32 -3.00 1.48e+00 4.57e-01 4.11e+00 ... (remaining 10367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 3945 17.14 - 34.28: 267 34.28 - 51.42: 46 51.42 - 68.55: 12 68.55 - 85.69: 4 Dihedral angle restraints: 4274 sinusoidal: 1603 harmonic: 2671 Sorted by residual: dihedral pdb=" CB GLU A 222 " pdb=" CG GLU A 222 " pdb=" CD GLU A 222 " pdb=" OE1 GLU A 222 " ideal model delta sinusoidal sigma weight residual 0.00 85.69 -85.69 1 3.00e+01 1.11e-03 9.87e+00 dihedral pdb=" CB GLU A 134 " pdb=" CG GLU A 134 " pdb=" CD GLU A 134 " pdb=" OE1 GLU A 134 " ideal model delta sinusoidal sigma weight residual 0.00 -85.53 85.53 1 3.00e+01 1.11e-03 9.84e+00 dihedral pdb=" CB MET C 294 " pdb=" CG MET C 294 " pdb=" SD MET C 294 " pdb=" CE MET C 294 " ideal model delta sinusoidal sigma weight residual 180.00 122.96 57.04 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 4271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1029 0.060 - 0.121: 141 0.121 - 0.181: 0 0.181 - 0.241: 0 0.241 - 0.302: 1 Chirality restraints: 1171 Sorted by residual: chirality pdb=" CA PHE B 7 " pdb=" N PHE B 7 " pdb=" C PHE B 7 " pdb=" CB PHE B 7 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA VAL A 279 " pdb=" N VAL A 279 " pdb=" C VAL A 279 " pdb=" CB VAL A 279 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.17e-01 chirality pdb=" CA PRO A 207 " pdb=" N PRO A 207 " pdb=" C PRO A 207 " pdb=" CB PRO A 207 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.16e-01 ... (remaining 1168 not shown) Planarity restraints: 1258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 231 " -0.028 2.00e-02 2.50e+03 1.91e-02 9.13e+00 pdb=" CG TRP B 231 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP B 231 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP B 231 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 231 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 231 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 231 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 231 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 231 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 231 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 231 " 0.022 2.00e-02 2.50e+03 1.35e-02 4.59e+00 pdb=" CG TRP A 231 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 231 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A 231 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 231 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 231 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 231 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 231 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 231 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 231 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 231 " 0.021 2.00e-02 2.50e+03 1.30e-02 4.25e+00 pdb=" CG TRP C 231 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP C 231 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP C 231 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 231 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 231 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 231 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 231 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 231 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 231 " 0.001 2.00e-02 2.50e+03 ... (remaining 1255 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 306 2.73 - 3.27: 8129 3.27 - 3.81: 13372 3.81 - 4.36: 16264 4.36 - 4.90: 28185 Nonbonded interactions: 66256 Sorted by model distance: nonbonded pdb=" NE1 TRP A 177 " pdb=" OE1 GLU A 181 " model vdw 2.186 3.120 nonbonded pdb=" O THR B 121 " pdb=" OG SER B 125 " model vdw 2.189 3.040 nonbonded pdb=" O THR C 121 " pdb=" OG SER C 125 " model vdw 2.191 3.040 nonbonded pdb=" NE1 TRP B 177 " pdb=" OE1 GLU B 181 " model vdw 2.201 3.120 nonbonded pdb=" O THR A 121 " pdb=" OG SER A 125 " model vdw 2.222 3.040 ... (remaining 66251 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' and (resid 6 through 283 or resid 285 through 313)) selection = (chain 'B' and (resid 6 through 283 or resid 285 through 313)) selection = (chain 'C' and (resid 6 through 283 or resid 285 through 313)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.900 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.290 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 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:17.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 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 : 0.002 0.027 7603 Z= 0.118 Angle : 0.436 4.553 10372 Z= 0.236 Chirality : 0.036 0.302 1171 Planarity : 0.003 0.026 1258 Dihedral : 12.322 85.692 2568 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.29), residues: 919 helix: 2.02 (0.20), residues: 745 sheet: None (None), residues: 0 loop : 0.18 (0.53), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 231 HIS 0.002 0.001 HIS A 163 PHE 0.010 0.001 PHE B 34 TYR 0.007 0.001 TYR A 304 ARG 0.001 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.819 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 1.0596 time to fit residues: 96.1733 Evaluate side-chains 63 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 292 ASN B 29 HIS C 29 HIS C 163 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7603 Z= 0.232 Angle : 0.513 6.196 10372 Z= 0.257 Chirality : 0.041 0.123 1171 Planarity : 0.004 0.037 1258 Dihedral : 3.796 16.738 992 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.17 % Allowed : 5.48 % Favored : 93.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.29), residues: 919 helix: 1.71 (0.19), residues: 754 sheet: None (None), residues: 0 loop : 0.26 (0.54), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 231 HIS 0.008 0.001 HIS B 29 PHE 0.012 0.001 PHE A 151 TYR 0.011 0.001 TYR B 304 ARG 0.005 0.001 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.687 Fit side-chains REVERT: A 219 ASN cc_start: 0.8036 (p0) cc_final: 0.7776 (p0) REVERT: B 219 ASN cc_start: 0.8133 (p0) cc_final: 0.7830 (p0) REVERT: B 222 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7198 (mt-10) REVERT: C 219 ASN cc_start: 0.8033 (p0) cc_final: 0.7822 (p0) outliers start: 9 outliers final: 3 residues processed: 83 average time/residue: 1.1517 time to fit residues: 101.6961 Evaluate side-chains 74 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain C residue 231 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN A 163 HIS B 163 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7603 Z= 0.244 Angle : 0.500 6.417 10372 Z= 0.250 Chirality : 0.040 0.123 1171 Planarity : 0.004 0.039 1258 Dihedral : 3.833 17.284 992 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.17 % Allowed : 6.27 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.28), residues: 919 helix: 1.89 (0.19), residues: 724 sheet: None (None), residues: 0 loop : 1.07 (0.48), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 231 HIS 0.002 0.001 HIS A 187 PHE 0.011 0.001 PHE A 262 TYR 0.008 0.001 TYR A 143 ARG 0.007 0.001 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 1.287 Fit side-chains REVERT: B 219 ASN cc_start: 0.8121 (p0) cc_final: 0.7818 (p0) REVERT: B 222 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7226 (mt-10) REVERT: C 219 ASN cc_start: 0.8020 (p0) cc_final: 0.7814 (p0) outliers start: 9 outliers final: 6 residues processed: 79 average time/residue: 1.1319 time to fit residues: 95.5403 Evaluate side-chains 78 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 231 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7603 Z= 0.196 Angle : 0.473 6.554 10372 Z= 0.237 Chirality : 0.039 0.119 1171 Planarity : 0.004 0.036 1258 Dihedral : 3.783 17.258 992 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.57 % Allowed : 6.14 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.28), residues: 919 helix: 1.58 (0.19), residues: 775 sheet: None (None), residues: 0 loop : 0.23 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 231 HIS 0.002 0.001 HIS A 187 PHE 0.010 0.001 PHE C 180 TYR 0.015 0.001 TYR C 304 ARG 0.007 0.001 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.757 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 85 average time/residue: 1.1255 time to fit residues: 102.6764 Evaluate side-chains 81 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 231 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7603 Z= 0.205 Angle : 0.477 6.304 10372 Z= 0.239 Chirality : 0.039 0.120 1171 Planarity : 0.004 0.037 1258 Dihedral : 3.799 17.333 992 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.57 % Allowed : 7.44 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.28), residues: 919 helix: 1.60 (0.19), residues: 775 sheet: None (None), residues: 0 loop : 0.29 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 231 HIS 0.002 0.001 HIS B 139 PHE 0.010 0.001 PHE C 180 TYR 0.007 0.001 TYR B 233 ARG 0.007 0.001 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.830 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 83 average time/residue: 1.0150 time to fit residues: 90.4081 Evaluate side-chains 82 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 231 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 72 optimal weight: 0.2980 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7603 Z= 0.178 Angle : 0.460 6.210 10372 Z= 0.231 Chirality : 0.038 0.117 1171 Planarity : 0.004 0.034 1258 Dihedral : 3.748 17.326 992 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.83 % Allowed : 6.92 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.28), residues: 919 helix: 1.66 (0.19), residues: 775 sheet: None (None), residues: 0 loop : 0.33 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 231 HIS 0.002 0.001 HIS B 187 PHE 0.009 0.001 PHE C 180 TYR 0.016 0.001 TYR B 304 ARG 0.008 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.806 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 87 average time/residue: 0.9905 time to fit residues: 92.4694 Evaluate side-chains 83 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 231 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 chunk 48 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7603 Z= 0.188 Angle : 0.466 6.326 10372 Z= 0.234 Chirality : 0.038 0.119 1171 Planarity : 0.004 0.037 1258 Dihedral : 3.755 17.342 992 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.57 % Allowed : 7.57 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.28), residues: 919 helix: 1.67 (0.19), residues: 775 sheet: None (None), residues: 0 loop : 0.40 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 231 HIS 0.002 0.001 HIS B 187 PHE 0.009 0.001 PHE C 180 TYR 0.016 0.001 TYR C 304 ARG 0.007 0.001 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.804 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 83 average time/residue: 0.9716 time to fit residues: 86.6098 Evaluate side-chains 84 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 231 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7603 Z= 0.196 Angle : 0.467 5.994 10372 Z= 0.235 Chirality : 0.039 0.120 1171 Planarity : 0.004 0.039 1258 Dihedral : 3.763 17.349 992 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.17 % Allowed : 7.83 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.28), residues: 919 helix: 1.65 (0.19), residues: 775 sheet: None (None), residues: 0 loop : 0.41 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 231 HIS 0.001 0.000 HIS A 187 PHE 0.010 0.001 PHE B 170 TYR 0.007 0.001 TYR B 233 ARG 0.007 0.001 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.744 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 83 average time/residue: 0.9936 time to fit residues: 88.5421 Evaluate side-chains 84 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 231 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 52 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7603 Z= 0.181 Angle : 0.460 6.071 10372 Z= 0.233 Chirality : 0.038 0.118 1171 Planarity : 0.004 0.038 1258 Dihedral : 3.744 17.301 992 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.17 % Allowed : 7.83 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.28), residues: 919 helix: 1.67 (0.19), residues: 775 sheet: None (None), residues: 0 loop : 0.42 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 231 HIS 0.002 0.000 HIS B 187 PHE 0.009 0.001 PHE C 180 TYR 0.016 0.001 TYR B 304 ARG 0.007 0.001 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.719 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 82 average time/residue: 1.0121 time to fit residues: 88.8140 Evaluate side-chains 82 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 231 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 0.0470 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7603 Z= 0.209 Angle : 0.477 5.961 10372 Z= 0.242 Chirality : 0.039 0.123 1171 Planarity : 0.004 0.044 1258 Dihedral : 3.785 17.389 992 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.17 % Allowed : 8.22 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.28), residues: 919 helix: 1.62 (0.19), residues: 775 sheet: None (None), residues: 0 loop : 0.46 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 231 HIS 0.001 0.001 HIS A 187 PHE 0.009 0.001 PHE B 170 TYR 0.018 0.001 TYR C 61 ARG 0.007 0.001 ARG A 243 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.790 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 81 average time/residue: 0.9909 time to fit residues: 86.1904 Evaluate side-chains 80 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 231 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 73 optimal weight: 0.0980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.0980 chunk 62 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.110556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.096283 restraints weight = 15435.043| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.93 r_work: 0.2792 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7603 Z= 0.156 Angle : 0.457 6.009 10372 Z= 0.234 Chirality : 0.038 0.116 1171 Planarity : 0.004 0.046 1258 Dihedral : 3.707 17.207 992 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.04 % Allowed : 8.36 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.28), residues: 919 helix: 1.69 (0.19), residues: 775 sheet: None (None), residues: 0 loop : 0.44 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 231 HIS 0.001 0.000 HIS A 187 PHE 0.010 0.001 PHE B 170 TYR 0.016 0.001 TYR C 61 ARG 0.007 0.001 ARG A 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2512.74 seconds wall clock time: 45 minutes 8.53 seconds (2708.53 seconds total)