Starting phenix.real_space_refine on Fri Jul 19 09:27:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi5_43249/07_2024/8vi5_43249.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi5_43249/07_2024/8vi5_43249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi5_43249/07_2024/8vi5_43249.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi5_43249/07_2024/8vi5_43249.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi5_43249/07_2024/8vi5_43249.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi5_43249/07_2024/8vi5_43249.cif" } resolution = 3.2 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= 0.013 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 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 31": "OE1" <-> "OE2" Residue "A PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "C PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 6.73, per 1000 atoms: 0.91 Number of scatterers: 7359 At special positions: 0 Unit cell: (91.126, 100.748, 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: 3.01 Conformation dependent library (CDL) restraints added in 1.9 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 89.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 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 removed outlier: 3.565A pdb=" N PHE A 82 " --> pdb=" O ARG A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 98 Processing helix chain 'A' and resid 101 through 123 Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.583A 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: 3.853A 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: 4.440A 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: 3.978A pdb=" N PHE A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.522A 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: 4.176A pdb=" N PHE A 262 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 4.442A 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 79 through 83 Processing helix chain 'B' and resid 84 through 98 Processing helix chain 'B' and resid 101 through 123 Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.665A 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: 3.819A 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: 4.480A 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: 3.999A pdb=" N PHE B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 249 removed outlier: 3.560A 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: 4.152A pdb=" N PHE B 262 " --> pdb=" O TRP B 258 " (cutoff:3.500A) removed outlier: 4.441A 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 removed outlier: 3.505A pdb=" N PHE C 82 " --> pdb=" O ARG C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 98 Processing helix chain 'C' and resid 101 through 123 Processing helix chain 'C' and resid 125 through 130 Processing helix chain 'C' and resid 134 through 138 removed outlier: 3.650A 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: 3.823A 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: 4.491A 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: 3.995A pdb=" N PHE C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 3.507A 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: 4.107A pdb=" N PHE C 262 " --> pdb=" O TRP C 258 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY C 263 " --> pdb=" O ALA C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 309 569 hydrogen bonds defined for protein. 1622 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: 2.23 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2010 1.33 - 1.45: 1457 1.45 - 1.57: 4085 1.57 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 7603 Sorted by residual: bond pdb=" N ARG B 243 " pdb=" CA ARG B 243 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.28e-02 6.10e+03 6.07e+00 bond pdb=" N ARG A 243 " pdb=" CA ARG A 243 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.33e-02 5.65e+03 5.79e+00 bond pdb=" N HIS A 163 " pdb=" CA HIS A 163 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.48e+00 bond pdb=" N HIS C 163 " pdb=" CA HIS C 163 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.23e-02 6.61e+03 5.35e+00 bond pdb=" N HIS B 163 " pdb=" CA HIS B 163 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.24e+00 ... (remaining 7598 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.14: 245 107.14 - 113.85: 4144 113.85 - 120.56: 3430 120.56 - 127.27: 2436 127.27 - 133.99: 117 Bond angle restraints: 10372 Sorted by residual: angle pdb=" CA PRO C 6 " pdb=" N PRO C 6 " pdb=" CD PRO C 6 " ideal model delta sigma weight residual 112.00 106.01 5.99 1.40e+00 5.10e-01 1.83e+01 angle pdb=" CA ARG A 64 " pdb=" C ARG A 64 " pdb=" O ARG A 64 " ideal model delta sigma weight residual 120.42 117.24 3.18 1.06e+00 8.90e-01 9.01e+00 angle pdb=" CA ARG A 71 " pdb=" C ARG A 71 " pdb=" O ARG A 71 " ideal model delta sigma weight residual 120.55 117.63 2.92 1.06e+00 8.90e-01 7.61e+00 angle pdb=" CA HIS A 163 " pdb=" C HIS A 163 " pdb=" O HIS A 163 " ideal model delta sigma weight residual 120.42 117.69 2.73 1.06e+00 8.90e-01 6.63e+00 angle pdb=" CA HIS C 163 " pdb=" C HIS C 163 " pdb=" O HIS C 163 " ideal model delta sigma weight residual 120.42 117.73 2.69 1.06e+00 8.90e-01 6.45e+00 ... (remaining 10367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 3918 17.03 - 34.06: 283 34.06 - 51.09: 55 51.09 - 68.11: 11 68.11 - 85.14: 7 Dihedral angle restraints: 4274 sinusoidal: 1603 harmonic: 2671 Sorted by residual: 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 90.00 132.90 -42.90 2 1.50e+01 4.44e-03 9.89e+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 -85.14 85.14 1 3.00e+01 1.11e-03 9.76e+00 dihedral pdb=" N PHE B 7 " pdb=" C PHE B 7 " pdb=" CA PHE B 7 " pdb=" CB PHE B 7 " ideal model delta harmonic sigma weight residual 122.80 130.58 -7.78 0 2.50e+00 1.60e-01 9.68e+00 ... (remaining 4271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1052 0.063 - 0.125: 115 0.125 - 0.188: 3 0.188 - 0.251: 0 0.251 - 0.314: 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 2.46e+00 chirality pdb=" CA ARG A 71 " pdb=" N ARG A 71 " pdb=" C ARG A 71 " pdb=" CB ARG A 71 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" CA ARG C 243 " pdb=" N ARG C 243 " pdb=" C ARG C 243 " pdb=" CB ARG C 243 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 1168 not shown) Planarity restraints: 1258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 231 " 0.023 2.00e-02 2.50e+03 1.54e-02 5.90e+00 pdb=" CG TRP B 231 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 231 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 231 " -0.001 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 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 231 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 231 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 231 " 0.002 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 1.51e-02 5.68e+00 pdb=" CG TRP C 231 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP C 231 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP C 231 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 231 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 231 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 231 " 0.002 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 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 231 " 0.023 2.00e-02 2.50e+03 1.50e-02 5.66e+00 pdb=" CG TRP A 231 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 231 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 231 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 231 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 231 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 231 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 231 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 231 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 231 " 0.002 2.00e-02 2.50e+03 ... (remaining 1255 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 18 2.39 - 3.02: 4629 3.02 - 3.65: 11693 3.65 - 4.27: 18013 4.27 - 4.90: 30978 Nonbonded interactions: 65331 Sorted by model distance: nonbonded pdb=" OE1 GLU C 68 " pdb=" NH2 ARG C 71 " model vdw 1.764 2.520 nonbonded pdb=" O THR B 121 " pdb=" OG SER B 125 " model vdw 2.085 2.440 nonbonded pdb=" O THR C 121 " pdb=" OG SER C 125 " model vdw 2.097 2.440 nonbonded pdb=" OE1 GLU C 68 " pdb=" NH1 ARG C 71 " model vdw 2.172 2.520 nonbonded pdb=" O THR A 121 " pdb=" OG SER A 125 " model vdw 2.216 2.440 ... (remaining 65326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 5.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 26.890 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 0.032 7603 Z= 0.186 Angle : 0.494 5.991 10372 Z= 0.283 Chirality : 0.038 0.314 1171 Planarity : 0.003 0.025 1258 Dihedral : 12.933 85.142 2568 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 2.79 (0.29), residues: 919 helix: 2.16 (0.20), residues: 718 sheet: None (None), residues: 0 loop : 0.85 (0.48), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 231 HIS 0.002 0.001 HIS B 276 PHE 0.010 0.001 PHE C 262 TYR 0.007 0.001 TYR A 143 ARG 0.002 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 80 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.841 Fit side-chains REVERT: A 71 ARG cc_start: 0.7372 (mtm180) cc_final: 0.6396 (mmp-170) REVERT: B 255 ILE cc_start: 0.9325 (mm) cc_final: 0.8886 (mm) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2069 time to fit residues: 22.4729 Evaluate side-chains 67 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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: 0.4980 chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.0770 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 0.1980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1069 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= 0.186 Angle : 0.483 5.890 10372 Z= 0.241 Chirality : 0.039 0.122 1171 Planarity : 0.003 0.022 1258 Dihedral : 3.607 17.863 992 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.52 % Allowed : 4.83 % Favored : 94.65 % 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: 2.29 (0.29), residues: 919 helix: 1.79 (0.19), residues: 775 sheet: None (None), residues: 0 loop : 0.22 (0.60), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 231 HIS 0.004 0.001 HIS A 187 PHE 0.013 0.001 PHE C 7 TYR 0.013 0.001 TYR A 66 ARG 0.002 0.000 ARG A 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 74 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.705 Fit side-chains REVERT: A 71 ARG cc_start: 0.7236 (mtm180) cc_final: 0.6194 (mmp-170) REVERT: C 103 LEU cc_start: 0.7995 (tt) cc_final: 0.7583 (mp) REVERT: C 201 MET cc_start: 0.8671 (mtp) cc_final: 0.8466 (mtp) outliers start: 4 outliers final: 0 residues processed: 72 average time/residue: 0.1964 time to fit residues: 19.3729 Evaluate side-chains 67 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 281 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1290 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= 0.210 Angle : 0.480 5.892 10372 Z= 0.236 Chirality : 0.039 0.126 1171 Planarity : 0.004 0.031 1258 Dihedral : 3.617 18.388 992 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.65 % Allowed : 5.09 % 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: 2.27 (0.28), residues: 919 helix: 1.83 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.09 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 231 HIS 0.003 0.001 HIS A 187 PHE 0.014 0.001 PHE C 7 TYR 0.010 0.001 TYR C 275 ARG 0.002 0.000 ARG C 71 *********************** 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 77 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.792 Fit side-chains REVERT: A 71 ARG cc_start: 0.7268 (mtm180) cc_final: 0.6231 (mmp-170) REVERT: C 103 LEU cc_start: 0.7990 (tt) cc_final: 0.7581 (mp) outliers start: 5 outliers final: 2 residues processed: 75 average time/residue: 0.2050 time to fit residues: 21.4377 Evaluate side-chains 69 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 TRP 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: 0.6980 chunk 42 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 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: 0.8123 moved from start: 0.1453 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= 0.209 Angle : 0.467 5.877 10372 Z= 0.231 Chirality : 0.039 0.127 1171 Planarity : 0.004 0.045 1258 Dihedral : 3.640 18.574 992 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.78 % Allowed : 5.22 % 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: 2.32 (0.28), residues: 919 helix: 1.87 (0.19), residues: 763 sheet: None (None), residues: 0 loop : 0.04 (0.55), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 231 HIS 0.003 0.001 HIS A 187 PHE 0.010 0.001 PHE A 34 TYR 0.011 0.001 TYR C 275 ARG 0.002 0.000 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 80 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.720 Fit side-chains REVERT: A 71 ARG cc_start: 0.7289 (mtm180) cc_final: 0.6298 (mmt-90) REVERT: C 39 MET cc_start: 0.6837 (tpp) cc_final: 0.6443 (tpp) REVERT: C 103 LEU cc_start: 0.8012 (tt) cc_final: 0.7611 (mp) outliers start: 6 outliers final: 4 residues processed: 79 average time/residue: 0.1972 time to fit residues: 21.6115 Evaluate side-chains 76 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 231 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1555 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= 0.182 Angle : 0.462 6.170 10372 Z= 0.227 Chirality : 0.038 0.139 1171 Planarity : 0.004 0.047 1258 Dihedral : 3.595 18.475 992 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.65 % Allowed : 6.66 % Favored : 92.69 % 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: 2.36 (0.28), residues: 919 helix: 1.86 (0.19), residues: 778 sheet: None (None), residues: 0 loop : 0.08 (0.58), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 231 HIS 0.002 0.001 HIS A 187 PHE 0.011 0.001 PHE A 34 TYR 0.009 0.001 TYR A 275 ARG 0.002 0.000 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 80 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.708 Fit side-chains REVERT: A 71 ARG cc_start: 0.7268 (mtm180) cc_final: 0.6266 (mmt-90) REVERT: B 79 ARG cc_start: 0.7813 (mtp180) cc_final: 0.7546 (mtm-85) REVERT: C 39 MET cc_start: 0.6808 (tpp) cc_final: 0.6433 (tpp) REVERT: C 103 LEU cc_start: 0.7998 (tt) cc_final: 0.7605 (mp) outliers start: 5 outliers final: 5 residues processed: 80 average time/residue: 0.2020 time to fit residues: 21.8854 Evaluate side-chains 78 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 57 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: 0.4980 chunk 21 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 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: 0.8127 moved from start: 0.1580 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= 0.210 Angle : 0.468 7.564 10372 Z= 0.230 Chirality : 0.039 0.150 1171 Planarity : 0.004 0.048 1258 Dihedral : 3.623 18.588 992 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.65 % Allowed : 6.66 % Favored : 92.69 % 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: 2.42 (0.28), residues: 919 helix: 1.94 (0.19), residues: 763 sheet: None (None), residues: 0 loop : 0.03 (0.55), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 231 HIS 0.002 0.001 HIS B 276 PHE 0.008 0.001 PHE B 28 TYR 0.007 0.001 TYR A 59 ARG 0.002 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 80 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.810 Fit side-chains REVERT: A 71 ARG cc_start: 0.7276 (mtm180) cc_final: 0.6268 (mmt-90) REVERT: B 79 ARG cc_start: 0.7833 (mtp180) cc_final: 0.7551 (mtm-85) REVERT: C 39 MET cc_start: 0.6897 (tpp) cc_final: 0.6504 (tpp) REVERT: C 103 LEU cc_start: 0.8026 (tt) cc_final: 0.7583 (mp) outliers start: 5 outliers final: 5 residues processed: 80 average time/residue: 0.2181 time to fit residues: 23.4564 Evaluate side-chains 81 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 57 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: 2.9990 chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 54 optimal weight: 0.2980 chunk 52 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN C 278 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7603 Z= 0.172 Angle : 0.467 7.584 10372 Z= 0.227 Chirality : 0.038 0.141 1171 Planarity : 0.004 0.049 1258 Dihedral : 3.556 18.683 992 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.65 % Allowed : 7.31 % Favored : 92.04 % 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: 2.51 (0.29), residues: 919 helix: 1.96 (0.19), residues: 778 sheet: None (None), residues: 0 loop : 0.13 (0.58), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 231 HIS 0.002 0.001 HIS A 187 PHE 0.013 0.001 PHE A 34 TYR 0.007 0.001 TYR A 59 ARG 0.002 0.000 ARG C 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 83 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 0.744 Fit side-chains REVERT: A 71 ARG cc_start: 0.7247 (mtm180) cc_final: 0.6237 (mmt-90) REVERT: B 79 ARG cc_start: 0.7803 (mtp180) cc_final: 0.7523 (mtm-85) REVERT: C 39 MET cc_start: 0.6903 (tpp) cc_final: 0.6535 (tpp) REVERT: C 103 LEU cc_start: 0.8005 (tt) cc_final: 0.7574 (mp) outliers start: 5 outliers final: 5 residues processed: 83 average time/residue: 0.2118 time to fit residues: 23.6950 Evaluate side-chains 77 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 57 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: 0.6980 chunk 17 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8116 moved from start: 0.1684 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= 0.195 Angle : 0.472 9.883 10372 Z= 0.228 Chirality : 0.039 0.143 1171 Planarity : 0.004 0.050 1258 Dihedral : 3.570 18.724 992 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.65 % Allowed : 7.18 % Favored : 92.17 % 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: 2.46 (0.29), residues: 919 helix: 1.93 (0.19), residues: 778 sheet: None (None), residues: 0 loop : 0.10 (0.58), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 231 HIS 0.002 0.001 HIS B 276 PHE 0.008 0.001 PHE B 28 TYR 0.007 0.001 TYR A 275 ARG 0.002 0.000 ARG C 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 82 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.643 Fit side-chains REVERT: A 71 ARG cc_start: 0.7251 (mtm180) cc_final: 0.6242 (mmt-90) REVERT: B 79 ARG cc_start: 0.7814 (mtp180) cc_final: 0.7527 (mtm-85) REVERT: C 39 MET cc_start: 0.6924 (tpp) cc_final: 0.6558 (tpp) REVERT: C 103 LEU cc_start: 0.8019 (tt) cc_final: 0.7583 (mp) outliers start: 5 outliers final: 5 residues processed: 82 average time/residue: 0.2021 time to fit residues: 22.6054 Evaluate side-chains 80 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 57 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: 0.4980 chunk 83 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN C 278 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1736 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= 0.198 Angle : 0.500 9.791 10372 Z= 0.240 Chirality : 0.039 0.142 1171 Planarity : 0.004 0.050 1258 Dihedral : 3.575 18.732 992 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.65 % Allowed : 7.31 % Favored : 92.04 % 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: 2.45 (0.29), residues: 919 helix: 1.92 (0.19), residues: 778 sheet: None (None), residues: 0 loop : 0.09 (0.57), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 231 HIS 0.002 0.001 HIS B 276 PHE 0.013 0.001 PHE A 34 TYR 0.007 0.001 TYR A 59 ARG 0.002 0.000 ARG C 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 79 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 0.781 Fit side-chains REVERT: A 71 ARG cc_start: 0.7252 (mtm180) cc_final: 0.6243 (mmt-90) REVERT: C 39 MET cc_start: 0.6927 (tpp) cc_final: 0.6549 (tpp) REVERT: C 103 LEU cc_start: 0.8022 (tt) cc_final: 0.7585 (mp) outliers start: 5 outliers final: 5 residues processed: 79 average time/residue: 0.2073 time to fit residues: 22.3378 Evaluate side-chains 78 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 57 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: 0.6980 chunk 89 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1689 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= 0.275 Angle : 0.512 9.939 10372 Z= 0.250 Chirality : 0.040 0.146 1171 Planarity : 0.004 0.049 1258 Dihedral : 3.702 19.127 992 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.65 % Allowed : 7.05 % 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: 2.31 (0.28), residues: 919 helix: 1.86 (0.19), residues: 763 sheet: None (None), residues: 0 loop : 0.05 (0.55), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 231 HIS 0.003 0.001 HIS B 276 PHE 0.010 0.001 PHE A 262 TYR 0.008 0.001 TYR A 233 ARG 0.002 0.000 ARG C 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 81 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.743 Fit side-chains REVERT: A 66 TYR cc_start: 0.8182 (m-10) cc_final: 0.7833 (m-10) REVERT: A 71 ARG cc_start: 0.7301 (mtm180) cc_final: 0.6282 (mmt-90) REVERT: C 39 MET cc_start: 0.7008 (tpp) cc_final: 0.6630 (tpp) REVERT: C 66 TYR cc_start: 0.8090 (m-10) cc_final: 0.7715 (m-10) REVERT: C 103 LEU cc_start: 0.8059 (tt) cc_final: 0.7850 (mt) outliers start: 5 outliers final: 5 residues processed: 81 average time/residue: 0.2080 time to fit residues: 22.9813 Evaluate side-chains 81 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 57 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: 1.9990 chunk 19 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.105329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.087252 restraints weight = 15877.699| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.09 r_work: 0.2708 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1720 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= 0.197 Angle : 0.504 9.720 10372 Z= 0.242 Chirality : 0.039 0.141 1171 Planarity : 0.004 0.051 1258 Dihedral : 3.633 18.940 992 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.65 % Allowed : 7.44 % Favored : 91.91 % 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: 2.35 (0.28), residues: 919 helix: 1.85 (0.19), residues: 778 sheet: None (None), residues: 0 loop : 0.07 (0.57), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 231 HIS 0.002 0.001 HIS B 276 PHE 0.009 0.001 PHE C 28 TYR 0.007 0.001 TYR A 59 ARG 0.002 0.000 ARG C 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1970.05 seconds wall clock time: 35 minutes 57.07 seconds (2157.07 seconds total)