Starting phenix.real_space_refine on Sat Aug 3 06:51:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi4_43248/08_2024/8vi4_43248.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi4_43248/08_2024/8vi4_43248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi4_43248/08_2024/8vi4_43248.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi4_43248/08_2024/8vi4_43248.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi4_43248/08_2024/8vi4_43248.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi4_43248/08_2024/8vi4_43248.cif" } resolution = 3.1 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= 0.015 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 TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s 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: 7.14, per 1000 atoms: 0.97 Number of scatterers: 7359 At special positions: 0 Unit cell: (100.182, 90.56, 61.694, 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: 3.13 Conformation dependent library (CDL) restraints added in 2.2 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 90.3% 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 79 through 83 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 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: 3.867A 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: 4.287A pdb=" N ALA A 199 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 203 Processing helix chain 'A' and resid 204 through 219 removed outlier: 4.731A pdb=" N ALA A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 3.852A 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: 3.991A pdb=" N PHE A 262 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 4.246A 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: 3.769A 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: 3.521A 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: 3.816A 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: 4.271A pdb=" N ALA B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 203 Processing helix chain 'B' and resid 204 through 219 removed outlier: 4.741A pdb=" N ALA B 208 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 249 removed outlier: 3.551A pdb=" N LYS B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) 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: 3.988A pdb=" N PHE B 262 " --> pdb=" O TRP B 258 " (cutoff:3.500A) removed outlier: 4.244A 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 79 through 83 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: 3.554A 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: 3.822A 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: 4.309A pdb=" N ALA C 199 " --> pdb=" O PRO C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 203 Processing helix chain 'C' and resid 204 through 219 removed outlier: 4.770A pdb=" N ALA C 208 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 3.662A 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: 4.020A pdb=" N PHE C 262 " --> pdb=" O TRP C 258 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY C 263 " --> pdb=" O ALA C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 309 572 hydrogen bonds defined for protein. 1631 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: 2.11 Time building geometry restraints manager: 3.44 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: 1613 1.46 - 1.57: 3785 1.57 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 7603 Sorted by residual: bond pdb=" CA SER C 191 " pdb=" CB SER C 191 " ideal model delta sigma weight residual 1.532 1.490 0.042 1.54e-02 4.22e+03 7.46e+00 bond pdb=" N SER C 191 " pdb=" CA SER C 191 " ideal model delta sigma weight residual 1.455 1.479 -0.024 1.09e-02 8.42e+03 4.65e+00 bond pdb=" N SER C 192 " pdb=" CA SER C 192 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.20e-02 6.94e+03 4.27e+00 bond pdb=" N LYS B 308 " pdb=" CA LYS B 308 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.31e-02 5.83e+03 4.24e+00 bond pdb=" N LEU C 193 " pdb=" CA LEU C 193 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 3.98e+00 ... (remaining 7598 not shown) Histogram of bond angle deviations from ideal: 100.60 - 107.28: 288 107.28 - 113.96: 4172 113.96 - 120.64: 3489 120.64 - 127.31: 2306 127.31 - 133.99: 117 Bond angle restraints: 10372 Sorted by residual: angle pdb=" CA ARG B 64 " pdb=" C ARG B 64 " pdb=" O ARG B 64 " ideal model delta sigma weight residual 120.70 117.07 3.63 1.03e+00 9.43e-01 1.24e+01 angle pdb=" C PHE B 7 " pdb=" CA PHE B 7 " pdb=" CB PHE B 7 " ideal model delta sigma weight residual 109.31 112.83 -3.52 1.23e+00 6.61e-01 8.19e+00 angle pdb=" CA SER C 191 " pdb=" C SER C 191 " pdb=" O SER C 191 " ideal model delta sigma weight residual 120.84 117.08 3.76 1.33e+00 5.65e-01 8.01e+00 angle pdb=" N LYS C 308 " pdb=" CA LYS C 308 " pdb=" CB LYS C 308 " ideal model delta sigma weight residual 110.41 105.77 4.64 1.68e+00 3.54e-01 7.62e+00 angle pdb=" N PHE B 7 " pdb=" CA PHE B 7 " pdb=" CB PHE B 7 " ideal model delta sigma weight residual 109.90 113.65 -3.75 1.54e+00 4.22e-01 5.94e+00 ... (remaining 10367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 3910 16.92 - 33.85: 297 33.85 - 50.77: 55 50.77 - 67.69: 10 67.69 - 84.62: 2 Dihedral angle restraints: 4274 sinusoidal: 1603 harmonic: 2671 Sorted by residual: dihedral pdb=" CA ILE B 190 " pdb=" C ILE B 190 " pdb=" N SER B 191 " pdb=" CA SER B 191 " ideal model delta harmonic sigma weight residual 180.00 -163.11 -16.89 0 5.00e+00 4.00e-02 1.14e+01 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 -84.62 84.62 1 3.00e+01 1.11e-03 9.67e+00 dihedral pdb=" CG ARG B 198 " pdb=" CD ARG B 198 " pdb=" NE ARG B 198 " pdb=" CZ ARG B 198 " ideal model delta sinusoidal sigma weight residual 90.00 132.05 -42.05 2 1.50e+01 4.44e-03 9.57e+00 ... (remaining 4271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1028 0.061 - 0.122: 139 0.122 - 0.183: 2 0.183 - 0.244: 1 0.244 - 0.305: 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 2.20 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA LYS C 308 " pdb=" N LYS C 308 " pdb=" C LYS C 308 " pdb=" CB LYS C 308 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA LYS B 308 " pdb=" N LYS B 308 " pdb=" C LYS B 308 " pdb=" CB LYS B 308 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 1168 not shown) Planarity restraints: 1258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 190 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.10e+00 pdb=" C ILE C 190 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE C 190 " -0.020 2.00e-02 2.50e+03 pdb=" N SER C 191 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 231 " -0.022 2.00e-02 2.50e+03 1.48e-02 5.46e+00 pdb=" CG TRP B 231 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP B 231 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP B 231 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 231 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 231 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 231 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 231 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 231 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 231 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 231 " 0.023 2.00e-02 2.50e+03 1.47e-02 5.42e+00 pdb=" CG TRP C 231 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP C 231 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP C 231 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 231 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 231 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 231 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 231 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 231 " -0.001 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: 2.13 - 2.69: 82 2.69 - 3.24: 7806 3.24 - 3.79: 12327 3.79 - 4.35: 17372 4.35 - 4.90: 28588 Nonbonded interactions: 66175 Sorted by model distance: nonbonded pdb=" O THR A 121 " pdb=" OG SER A 125 " model vdw 2.132 3.040 nonbonded pdb=" O THR C 121 " pdb=" OG SER C 125 " model vdw 2.137 3.040 nonbonded pdb=" O THR B 121 " pdb=" OG SER B 125 " model vdw 2.150 3.040 nonbonded pdb=" NE1 TRP A 177 " pdb=" OE1 GLU A 181 " model vdw 2.171 3.120 nonbonded pdb=" NE1 TRP B 177 " pdb=" OE1 GLU B 181 " model vdw 2.186 3.120 ... (remaining 66170 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: 4.660 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.600 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 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 0.042 7603 Z= 0.159 Angle : 0.463 4.725 10372 Z= 0.260 Chirality : 0.038 0.305 1171 Planarity : 0.003 0.030 1258 Dihedral : 12.375 84.619 2568 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.13 % Allowed : 0.26 % Favored : 99.61 % 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: 2.48 (0.29), residues: 919 helix: 2.08 (0.20), residues: 724 sheet: None (None), residues: 0 loop : 0.06 (0.48), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 231 HIS 0.003 0.001 HIS A 163 PHE 0.014 0.001 PHE C 288 TYR 0.004 0.001 TYR C 143 ARG 0.003 0.000 ARG B 79 *********************** 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 72 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.780 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.1917 time to fit residues: 19.3957 Evaluate side-chains 67 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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: 0.6980 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 81 optimal weight: 0.4980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS B 163 HIS C 163 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7603 Z= 0.235 Angle : 0.492 5.972 10372 Z= 0.251 Chirality : 0.040 0.121 1171 Planarity : 0.004 0.024 1258 Dihedral : 3.778 16.215 992 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.65 % Allowed : 2.09 % Favored : 97.26 % 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: 2.33 (0.28), residues: 919 helix: 1.87 (0.19), residues: 733 sheet: None (None), residues: 0 loop : 0.40 (0.52), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 231 HIS 0.002 0.001 HIS B 187 PHE 0.015 0.001 PHE A 274 TYR 0.012 0.001 TYR A 304 ARG 0.005 0.001 ARG A 79 *********************** 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 84 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.715 Fit side-chains REVERT: B 231 TRP cc_start: 0.8503 (OUTLIER) cc_final: 0.8139 (m-10) outliers start: 5 outliers final: 4 residues processed: 84 average time/residue: 0.1709 time to fit residues: 20.2137 Evaluate side-chains 76 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 193 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: 3.9990 chunk 25 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7603 Z= 0.232 Angle : 0.475 5.930 10372 Z= 0.242 Chirality : 0.039 0.118 1171 Planarity : 0.004 0.026 1258 Dihedral : 3.791 16.679 992 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.78 % Allowed : 3.52 % Favored : 95.69 % 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: 2.24 (0.28), residues: 919 helix: 1.78 (0.19), residues: 739 sheet: None (None), residues: 0 loop : 0.45 (0.53), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 231 HIS 0.003 0.001 HIS B 187 PHE 0.010 0.001 PHE A 274 TYR 0.011 0.001 TYR A 304 ARG 0.004 0.000 ARG A 79 *********************** 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 80 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.798 Fit side-chains REVERT: A 114 ILE cc_start: 0.8254 (mt) cc_final: 0.8052 (mm) REVERT: B 231 TRP cc_start: 0.8530 (OUTLIER) cc_final: 0.8005 (m-10) REVERT: C 196 GLN cc_start: 0.8912 (pm20) cc_final: 0.8659 (pm20) outliers start: 6 outliers final: 3 residues processed: 80 average time/residue: 0.1859 time to fit residues: 21.0123 Evaluate side-chains 78 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 193 LEU 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: 0.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.8431 moved from start: 0.1316 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= 0.211 Angle : 0.461 5.858 10372 Z= 0.234 Chirality : 0.039 0.116 1171 Planarity : 0.004 0.029 1258 Dihedral : 3.753 16.567 992 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.04 % Allowed : 3.79 % Favored : 95.17 % 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: 2.28 (0.28), residues: 919 helix: 1.76 (0.19), residues: 754 sheet: None (None), residues: 0 loop : 0.62 (0.56), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 231 HIS 0.002 0.000 HIS B 187 PHE 0.010 0.001 PHE A 274 TYR 0.011 0.001 TYR A 304 ARG 0.004 0.000 ARG B 79 *********************** 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 87 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.845 Fit side-chains REVERT: B 231 TRP cc_start: 0.8472 (OUTLIER) cc_final: 0.7925 (m-10) REVERT: C 196 GLN cc_start: 0.8894 (pm20) cc_final: 0.8643 (pm20) outliers start: 8 outliers final: 6 residues processed: 85 average time/residue: 0.1758 time to fit residues: 21.4838 Evaluate side-chains 83 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 193 LEU 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: 0.5980 chunk 35 optimal weight: 0.3980 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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: 0.8423 moved from start: 0.1417 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= 0.194 Angle : 0.448 5.814 10372 Z= 0.228 Chirality : 0.038 0.116 1171 Planarity : 0.004 0.030 1258 Dihedral : 3.706 16.568 992 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.31 % Allowed : 3.92 % Favored : 94.78 % 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: 2.36 (0.28), residues: 919 helix: 1.82 (0.19), residues: 754 sheet: None (None), residues: 0 loop : 0.60 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 231 HIS 0.002 0.000 HIS B 187 PHE 0.009 0.001 PHE A 274 TYR 0.009 0.001 TYR A 304 ARG 0.005 0.000 ARG A 79 *********************** 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 87 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.836 Fit side-chains REVERT: B 231 TRP cc_start: 0.8438 (OUTLIER) cc_final: 0.7843 (m-10) REVERT: C 196 GLN cc_start: 0.8884 (pm20) cc_final: 0.8631 (pm20) outliers start: 10 outliers final: 9 residues processed: 82 average time/residue: 0.2066 time to fit residues: 23.7511 Evaluate side-chains 85 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 193 LEU 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: 3.9990 chunk 21 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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: 0.8458 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7603 Z= 0.258 Angle : 0.477 6.116 10372 Z= 0.241 Chirality : 0.039 0.122 1171 Planarity : 0.004 0.030 1258 Dihedral : 3.807 17.055 992 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.31 % Allowed : 3.79 % Favored : 94.91 % 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: 2.24 (0.28), residues: 919 helix: 1.78 (0.19), residues: 739 sheet: None (None), residues: 0 loop : 0.44 (0.52), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 231 HIS 0.002 0.001 HIS A 187 PHE 0.009 0.001 PHE A 34 TYR 0.008 0.001 TYR A 304 ARG 0.005 0.001 ARG A 79 *********************** 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 83 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.875 Fit side-chains REVERT: B 231 TRP cc_start: 0.8562 (OUTLIER) cc_final: 0.7931 (m-10) REVERT: C 196 GLN cc_start: 0.8909 (pm20) cc_final: 0.8657 (pm20) outliers start: 10 outliers final: 7 residues processed: 79 average time/residue: 0.1825 time to fit residues: 20.5098 Evaluate side-chains 80 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 193 LEU 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: 0.6980 chunk 49 optimal weight: 0.2980 chunk 73 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.8423 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7603 Z= 0.181 Angle : 0.445 5.780 10372 Z= 0.225 Chirality : 0.038 0.116 1171 Planarity : 0.004 0.030 1258 Dihedral : 3.697 16.703 992 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.31 % Allowed : 3.92 % Favored : 94.78 % 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: 2.39 (0.28), residues: 919 helix: 1.84 (0.19), residues: 754 sheet: None (None), residues: 0 loop : 0.60 (0.54), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 231 HIS 0.002 0.000 HIS B 187 PHE 0.009 0.001 PHE A 274 TYR 0.008 0.001 TYR A 304 ARG 0.004 0.000 ARG B 79 *********************** 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: 10 poor density : 79 time to evaluate : 0.922 Fit side-chains REVERT: B 231 TRP cc_start: 0.8430 (OUTLIER) cc_final: 0.7826 (m-10) REVERT: C 196 GLN cc_start: 0.8882 (pm20) cc_final: 0.8622 (pm20) outliers start: 10 outliers final: 8 residues processed: 84 average time/residue: 0.1823 time to fit residues: 21.7090 Evaluate side-chains 85 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 159 LEU 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: 4.9990 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 42 optimal weight: 0.0270 chunk 8 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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: 0.8423 moved from start: 0.1553 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= 0.187 Angle : 0.451 6.605 10372 Z= 0.227 Chirality : 0.038 0.115 1171 Planarity : 0.004 0.030 1258 Dihedral : 3.682 16.677 992 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.31 % Allowed : 4.18 % Favored : 94.52 % 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: 2.42 (0.28), residues: 919 helix: 1.86 (0.19), residues: 754 sheet: None (None), residues: 0 loop : 0.59 (0.54), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 231 HIS 0.002 0.000 HIS B 187 PHE 0.008 0.001 PHE A 274 TYR 0.007 0.001 TYR A 304 ARG 0.005 0.000 ARG B 79 *********************** 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: 10 poor density : 76 time to evaluate : 0.841 Fit side-chains REVERT: B 231 TRP cc_start: 0.8423 (OUTLIER) cc_final: 0.7795 (m-10) outliers start: 10 outliers final: 9 residues processed: 81 average time/residue: 0.1792 time to fit residues: 20.6736 Evaluate side-chains 85 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 159 LEU 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: 0.5980 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 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: 0.8430 moved from start: 0.1567 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= 0.201 Angle : 0.451 6.459 10372 Z= 0.228 Chirality : 0.038 0.116 1171 Planarity : 0.004 0.030 1258 Dihedral : 3.691 16.685 992 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.17 % Allowed : 4.57 % Favored : 94.26 % 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: 2.41 (0.28), residues: 919 helix: 1.86 (0.19), residues: 754 sheet: None (None), residues: 0 loop : 0.56 (0.54), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 231 HIS 0.002 0.001 HIS B 29 PHE 0.008 0.001 PHE A 274 TYR 0.007 0.001 TYR B 233 ARG 0.005 0.000 ARG A 79 *********************** 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 84 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.818 Fit side-chains REVERT: B 231 TRP cc_start: 0.8457 (OUTLIER) cc_final: 0.7846 (m-10) outliers start: 9 outliers final: 8 residues processed: 80 average time/residue: 0.1850 time to fit residues: 20.9895 Evaluate side-chains 84 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 159 LEU 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: 1.9990 chunk 59 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 chunk 56 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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: 0.8408 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7603 Z= 0.166 Angle : 0.443 6.370 10372 Z= 0.222 Chirality : 0.037 0.116 1171 Planarity : 0.004 0.030 1258 Dihedral : 3.633 16.541 992 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.17 % Allowed : 4.83 % Favored : 93.99 % 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: 2.54 (0.28), residues: 919 helix: 1.95 (0.19), residues: 754 sheet: None (None), residues: 0 loop : 0.59 (0.54), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 231 HIS 0.002 0.000 HIS B 29 PHE 0.008 0.001 PHE A 274 TYR 0.006 0.001 TYR A 304 ARG 0.005 0.000 ARG A 79 ********************** 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 86 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.721 Fit side-chains REVERT: A 79 ARG cc_start: 0.8706 (mtp85) cc_final: 0.8426 (mtp180) REVERT: B 231 TRP cc_start: 0.8379 (OUTLIER) cc_final: 0.7752 (m-10) outliers start: 9 outliers final: 7 residues processed: 82 average time/residue: 0.1766 time to fit residues: 20.5238 Evaluate side-chains 83 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 159 LEU 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: 0.6980 chunk 10 optimal weight: 0.2980 chunk 19 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 73 optimal weight: 0.0010 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 62 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 overall best weight: 0.4386 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.122593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.106457 restraints weight = 14942.828| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.98 r_work: 0.3049 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7603 Z= 0.158 Angle : 0.437 6.356 10372 Z= 0.220 Chirality : 0.037 0.115 1171 Planarity : 0.004 0.030 1258 Dihedral : 3.594 16.375 992 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.04 % Allowed : 4.96 % Favored : 93.99 % 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: 3.07 (0.28), residues: 919 helix: 2.27 (0.19), residues: 724 sheet: None (None), residues: 0 loop : 1.31 (0.50), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 231 HIS 0.002 0.000 HIS B 187 PHE 0.008 0.001 PHE A 274 TYR 0.006 0.001 TYR B 233 ARG 0.005 0.000 ARG A 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1933.84 seconds wall clock time: 35 minutes 50.60 seconds (2150.60 seconds total)