Starting phenix.real_space_refine on Sat Aug 3 06:58:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi2_43246/08_2024/8vi2_43246.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi2_43246/08_2024/8vi2_43246.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/8vi2_43246/08_2024/8vi2_43246.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi2_43246/08_2024/8vi2_43246.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi2_43246/08_2024/8vi2_43246.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi2_43246/08_2024/8vi2_43246.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= 0.013 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 5004 2.51 5 N 1141 2.21 5 O 1210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "C PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7382 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2473 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 308, 2449 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 13, 'TRANS': 294} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 308, 2452 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 13, 'TRANS': 294} bond proxies already assigned to first conformer: 2507 Conformer: "C" Number of residues, atoms: 307, 2434 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 13, 'TRANS': 293} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved chain link dihedrals: 12 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 bond proxies already assigned to first conformer: 2507 Chain: "B" Number of atoms: 2457 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: 2527 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} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLU A 69 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 69 " occ=0.50 Time building chain proxies: 9.82, per 1000 atoms: 1.33 Number of scatterers: 7382 At special positions: 0 Unit cell: (92.258, 100.748, 62.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 1210 8.00 N 1141 7.00 C 5004 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: 3.47 Conformation dependent library (CDL) restraints added in 3.1 seconds 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 0 sheets defined 90.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 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 34 through 66 removed outlier: 3.883A pdb=" N ARG A 38 " --> pdb=" O PHE A 34 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.973A pdb=" N ILE A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 79 through 84' Processing helix chain 'A' and resid 84 through 98 Processing helix chain 'A' and resid 101 through 124 Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.747A 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: 3.827A 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 191 Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 194 through 204 removed outlier: 4.734A pdb=" N ALA A 199 " --> pdb=" O GLN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 219 removed outlier: 3.989A pdb=" N PHE A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.787A 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 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 257 through 277 removed outlier: 4.002A pdb=" N SER A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE A 262 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 273 " --> pdb=" O ASN A 269 " (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 34 through 66 removed outlier: 3.877A pdb=" N ARG B 38 " --> pdb=" O PHE B 34 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET B 39 " --> pdb=" O PRO B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 76 Processing helix chain 'B' and resid 79 through 84 removed outlier: 3.943A pdb=" N ILE B 83 " --> pdb=" O ARG B 79 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA B 84 " --> pdb=" O PHE B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 84' 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: 3.746A 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: 3.830A 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: 4.381A 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: 3.996A pdb=" N PHE B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 249 Proline residue: B 246 - end of helix Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 257 through 277 removed outlier: 3.994A pdb=" N SER B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE B 262 " --> pdb=" O TRP B 258 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 273 " --> pdb=" O ASN B 269 " (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 34 through 66 removed outlier: 3.844A pdb=" N ARG C 38 " --> pdb=" O PHE C 34 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET C 39 " --> pdb=" O PRO C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 79 through 84 removed outlier: 3.958A pdb=" N ILE C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 79 through 84' 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: 3.853A 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: 3.818A 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 204 removed outlier: 4.711A pdb=" N ALA C 199 " --> pdb=" O GLN C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 219 removed outlier: 3.942A pdb=" N PHE C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 3.888A 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 256 No H-bonds generated for 'chain 'C' and resid 254 through 256' Processing helix chain 'C' and resid 257 through 277 removed outlier: 4.021A pdb=" N SER C 261 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE C 262 " --> pdb=" O TRP C 258 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLY C 263 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 273 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 309 570 hydrogen bonds defined for protein. 1614 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: 2.28 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1279 1.33 - 1.45: 2150 1.45 - 1.57: 4151 1.57 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 7631 Sorted by residual: bond pdb=" N LEU B 9 " pdb=" CA LEU B 9 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.13e-02 7.83e+03 1.04e+01 bond pdb=" N PHE B 7 " pdb=" CA PHE B 7 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.14e-02 7.69e+03 7.32e+00 bond pdb=" N PHE C 7 " pdb=" CA PHE C 7 " ideal model delta sigma weight residual 1.453 1.484 -0.030 1.16e-02 7.43e+03 6.83e+00 bond pdb=" N LEU C 9 " pdb=" CA LEU C 9 " ideal model delta sigma weight residual 1.462 1.491 -0.030 1.19e-02 7.06e+03 6.23e+00 bond pdb=" N LEU A 9 " pdb=" CA LEU A 9 " ideal model delta sigma weight residual 1.462 1.489 -0.028 1.19e-02 7.06e+03 5.43e+00 ... (remaining 7626 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.51: 241 106.51 - 113.38: 4033 113.38 - 120.25: 3071 120.25 - 127.13: 2962 127.13 - 134.00: 111 Bond angle restraints: 10418 Sorted by residual: angle pdb=" C PRO C 8 " pdb=" N LEU C 9 " pdb=" CA LEU C 9 " ideal model delta sigma weight residual 123.46 117.62 5.84 1.35e+00 5.49e-01 1.87e+01 angle pdb=" N PRO B 10 " pdb=" CA PRO B 10 " pdb=" C PRO B 10 " ideal model delta sigma weight residual 110.80 105.24 5.56 1.51e+00 4.39e-01 1.36e+01 angle pdb=" C LEU C 9 " pdb=" N PRO C 10 " pdb=" CA PRO C 10 " ideal model delta sigma weight residual 119.90 123.63 -3.73 1.02e+00 9.61e-01 1.34e+01 angle pdb=" C LEU A 9 " pdb=" N PRO A 10 " pdb=" CA PRO A 10 " ideal model delta sigma weight residual 119.90 122.98 -3.08 1.02e+00 9.61e-01 9.12e+00 angle pdb=" CA PRO B 10 " pdb=" C PRO B 10 " pdb=" O PRO B 10 " ideal model delta sigma weight residual 121.03 117.61 3.42 1.14e+00 7.69e-01 8.98e+00 ... (remaining 10413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 3951 17.28 - 34.57: 293 34.57 - 51.85: 44 51.85 - 69.14: 11 69.14 - 86.42: 3 Dihedral angle restraints: 4302 sinusoidal: 1611 harmonic: 2691 Sorted by residual: 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 -86.42 86.42 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" CB LYS C 251 " pdb=" CG LYS C 251 " pdb=" CD LYS C 251 " pdb=" CE LYS C 251 " ideal model delta sinusoidal sigma weight residual 180.00 121.07 58.93 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB LYS A 251 " pdb=" CG LYS A 251 " pdb=" CD LYS A 251 " pdb=" CE LYS A 251 " ideal model delta sinusoidal sigma weight residual 180.00 121.09 58.91 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 4299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 849 0.031 - 0.062: 187 0.062 - 0.092: 110 0.092 - 0.123: 27 0.123 - 0.154: 4 Chirality restraints: 1177 Sorted by residual: chirality pdb=" CA PRO B 10 " pdb=" N PRO B 10 " pdb=" C PRO B 10 " pdb=" CB PRO B 10 " both_signs ideal model delta sigma weight residual False 2.72 2.87 -0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CB ILE A 218 " pdb=" CA ILE A 218 " pdb=" CG1 ILE A 218 " pdb=" CG2 ILE A 218 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA PRO B 207 " pdb=" N PRO B 207 " pdb=" C PRO B 207 " pdb=" CB PRO B 207 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 1174 not shown) Planarity restraints: 1265 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 206 " -0.037 5.00e-02 4.00e+02 5.64e-02 5.08e+00 pdb=" N PRO B 207 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 207 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 207 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 231 " -0.021 2.00e-02 2.50e+03 1.37e-02 4.71e+00 pdb=" CG TRP B 231 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B 231 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP B 231 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 231 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 231 " -0.003 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 " 0.001 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 " -0.020 2.00e-02 2.50e+03 1.32e-02 4.34e+00 pdb=" CG TRP C 231 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP C 231 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP C 231 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 231 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 231 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 231 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 231 " -0.003 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 1262 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 43 2.60 - 3.18: 7397 3.18 - 3.75: 12073 3.75 - 4.33: 17340 4.33 - 4.90: 29133 Nonbonded interactions: 65986 Sorted by model distance: nonbonded pdb=" O THR B 121 " pdb=" OG SER B 125 " model vdw 2.029 3.040 nonbonded pdb=" O THR C 121 " pdb=" OG SER C 125 " model vdw 2.053 3.040 nonbonded pdb=" O THR A 121 " pdb=" OG SER A 125 " model vdw 2.063 3.040 nonbonded pdb=" OH TYR B 215 " pdb=" OD2 ASP B 224 " model vdw 2.095 3.040 nonbonded pdb=" OH TYR C 13 " pdb=" O PHE C 311 " model vdw 2.113 3.040 ... (remaining 65981 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 68 or resid 70 through 102 or resid 104 through \ 119 or resid 121 through 154 or resid 156 through 283 or resid 285 through 290 o \ r resid 292 through 313)) selection = (chain 'B' and (resid 6 through 68 or resid 70 through 102 or resid 104 through \ 119 or resid 121 through 154 or resid 156 through 283 or resid 285 through 290 o \ r resid 292 through 313)) selection = (chain 'C' and (resid 6 through 68 or resid 70 through 102 or resid 104 through \ 119 or resid 121 through 154 or resid 156 through 283 or resid 285 through 290 o \ r resid 292 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=0.47 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: 6.640 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 33.360 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 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 0.036 7631 Z= 0.172 Angle : 0.484 5.840 10418 Z= 0.284 Chirality : 0.036 0.154 1177 Planarity : 0.005 0.056 1265 Dihedral : 12.423 86.422 2586 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: 0.67 (0.29), residues: 926 helix: 0.49 (0.21), residues: 699 sheet: None (None), residues: 0 loop : 0.77 (0.44), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 231 HIS 0.002 0.000 HIS A 163 PHE 0.013 0.001 PHE C 7 TYR 0.014 0.001 TYR A 167 ARG 0.002 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.794 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1943 time to fit residues: 19.5981 Evaluate side-chains 66 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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: 0.7980 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 0.0060 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 163 HIS A 276 HIS B 163 HIS B 276 HIS C 163 HIS C 276 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7631 Z= 0.234 Angle : 0.514 5.879 10418 Z= 0.266 Chirality : 0.041 0.151 1177 Planarity : 0.005 0.054 1265 Dihedral : 3.684 19.425 1002 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.13 % Allowed : 3.63 % Favored : 96.24 % 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: 3.01 (0.28), residues: 926 helix: 2.06 (0.19), residues: 711 sheet: None (None), residues: 0 loop : 2.08 (0.50), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 231 HIS 0.002 0.001 HIS A 187 PHE 0.013 0.001 PHE C 7 TYR 0.018 0.001 TYR C 167 ARG 0.003 0.001 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.817 Fit side-chains REVERT: A 79 ARG cc_start: 0.8863 (mtp85) cc_final: 0.8559 (mtp-110) REVERT: C 278 ASN cc_start: 0.8660 (t0) cc_final: 0.8442 (t0) outliers start: 1 outliers final: 1 residues processed: 75 average time/residue: 0.2144 time to fit residues: 21.6489 Evaluate side-chains 73 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 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: 0.8184 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7631 Z= 0.225 Angle : 0.496 7.052 10418 Z= 0.251 Chirality : 0.040 0.142 1177 Planarity : 0.004 0.055 1265 Dihedral : 3.694 19.034 1002 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.52 % Allowed : 4.54 % Favored : 94.94 % 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: 3.38 (0.29), residues: 926 helix: 2.47 (0.19), residues: 704 sheet: None (None), residues: 0 loop : 1.66 (0.50), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 231 HIS 0.004 0.001 HIS A 29 PHE 0.011 0.001 PHE A 288 TYR 0.014 0.001 TYR C 167 ARG 0.006 0.001 ARG C 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.856 Fit side-chains REVERT: A 79 ARG cc_start: 0.8881 (mtp85) cc_final: 0.8589 (mtp-110) REVERT: C 201 MET cc_start: 0.8577 (mmm) cc_final: 0.8331 (tpp) REVERT: C 278 ASN cc_start: 0.8790 (t0) cc_final: 0.8525 (t0) outliers start: 4 outliers final: 4 residues processed: 76 average time/residue: 0.2373 time to fit residues: 24.0721 Evaluate side-chains 76 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 231 TRP 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: 0.8980 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 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: 0.8194 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7631 Z= 0.216 Angle : 0.479 6.920 10418 Z= 0.241 Chirality : 0.040 0.142 1177 Planarity : 0.004 0.052 1265 Dihedral : 3.684 19.374 1002 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.65 % Allowed : 4.41 % Favored : 94.94 % 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: 3.48 (0.29), residues: 926 helix: 2.56 (0.20), residues: 704 sheet: None (None), residues: 0 loop : 1.61 (0.50), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 231 HIS 0.003 0.001 HIS B 29 PHE 0.011 0.001 PHE A 288 TYR 0.011 0.001 TYR C 167 ARG 0.005 0.001 ARG C 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.771 Fit side-chains REVERT: A 79 ARG cc_start: 0.8892 (mtp85) cc_final: 0.8590 (mtp-110) REVERT: C 201 MET cc_start: 0.8577 (mmm) cc_final: 0.8314 (tpp) REVERT: C 278 ASN cc_start: 0.8772 (t0) cc_final: 0.8519 (t0) outliers start: 5 outliers final: 3 residues processed: 82 average time/residue: 0.2336 time to fit residues: 25.6154 Evaluate side-chains 76 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 231 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.8204 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7631 Z= 0.225 Angle : 0.483 5.681 10418 Z= 0.243 Chirality : 0.039 0.140 1177 Planarity : 0.004 0.053 1265 Dihedral : 3.707 19.257 1002 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.52 % Allowed : 5.19 % Favored : 94.29 % 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: 3.24 (0.29), residues: 926 helix: 2.40 (0.20), residues: 718 sheet: None (None), residues: 0 loop : 1.41 (0.52), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 231 HIS 0.003 0.001 HIS A 187 PHE 0.011 0.001 PHE A 288 TYR 0.010 0.001 TYR C 167 ARG 0.005 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.784 Fit side-chains REVERT: A 79 ARG cc_start: 0.8891 (mtp85) cc_final: 0.8582 (mtp-110) REVERT: C 201 MET cc_start: 0.8572 (mmm) cc_final: 0.8302 (tpp) REVERT: C 278 ASN cc_start: 0.8783 (t0) cc_final: 0.8540 (t0) outliers start: 4 outliers final: 4 residues processed: 79 average time/residue: 0.2200 time to fit residues: 23.2156 Evaluate side-chains 78 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 231 TRP Chi-restraints excluded: chain C residue 302 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 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: 0.8194 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7631 Z= 0.201 Angle : 0.470 6.298 10418 Z= 0.237 Chirality : 0.039 0.138 1177 Planarity : 0.004 0.053 1265 Dihedral : 3.673 19.031 1002 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.39 % Allowed : 5.58 % Favored : 94.03 % 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: 3.27 (0.29), residues: 926 helix: 2.41 (0.20), residues: 721 sheet: None (None), residues: 0 loop : 1.44 (0.52), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 231 HIS 0.003 0.000 HIS B 29 PHE 0.011 0.001 PHE A 288 TYR 0.009 0.001 TYR C 167 ARG 0.005 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.778 Fit side-chains REVERT: A 79 ARG cc_start: 0.8891 (mtp85) cc_final: 0.8584 (mtp-110) REVERT: C 201 MET cc_start: 0.8564 (mmm) cc_final: 0.8284 (tpp) REVERT: C 278 ASN cc_start: 0.8767 (t0) cc_final: 0.8543 (t0) outliers start: 3 outliers final: 3 residues processed: 79 average time/residue: 0.2165 time to fit residues: 23.0378 Evaluate side-chains 76 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 231 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7631 Z= 0.203 Angle : 0.478 7.642 10418 Z= 0.237 Chirality : 0.039 0.138 1177 Planarity : 0.004 0.052 1265 Dihedral : 3.664 19.087 1002 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.52 % Allowed : 5.84 % Favored : 93.64 % 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: 3.28 (0.29), residues: 926 helix: 2.43 (0.20), residues: 721 sheet: None (None), residues: 0 loop : 1.40 (0.51), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 231 HIS 0.002 0.000 HIS B 29 PHE 0.010 0.001 PHE A 288 TYR 0.008 0.001 TYR A 59 ARG 0.005 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.801 Fit side-chains REVERT: A 79 ARG cc_start: 0.8885 (mtp85) cc_final: 0.8572 (mtp-110) REVERT: C 201 MET cc_start: 0.8564 (mmm) cc_final: 0.8294 (tpp) outliers start: 4 outliers final: 4 residues processed: 78 average time/residue: 0.2285 time to fit residues: 23.7779 Evaluate side-chains 76 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 231 TRP Chi-restraints excluded: chain C residue 302 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 0.0980 chunk 8 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 78 optimal weight: 0.0670 chunk 83 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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: 0.8174 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7631 Z= 0.171 Angle : 0.460 6.463 10418 Z= 0.230 Chirality : 0.038 0.133 1177 Planarity : 0.004 0.053 1265 Dihedral : 3.616 18.672 1002 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.52 % Allowed : 5.71 % Favored : 93.77 % 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: 3.41 (0.29), residues: 926 helix: 2.52 (0.20), residues: 721 sheet: None (None), residues: 0 loop : 1.44 (0.52), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 231 HIS 0.003 0.000 HIS B 29 PHE 0.011 0.001 PHE A 288 TYR 0.008 0.001 TYR A 59 ARG 0.005 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 0.902 Fit side-chains REVERT: A 79 ARG cc_start: 0.8886 (mtp85) cc_final: 0.8582 (mtp-110) REVERT: B 198 ARG cc_start: 0.8094 (mtt180) cc_final: 0.7624 (mtt180) REVERT: C 79 ARG cc_start: 0.8920 (mtp85) cc_final: 0.8622 (mtp-110) REVERT: C 153 SER cc_start: 0.8393 (m) cc_final: 0.8127 (m) REVERT: C 201 MET cc_start: 0.8551 (mmm) cc_final: 0.8277 (tpp) outliers start: 4 outliers final: 4 residues processed: 90 average time/residue: 0.2045 time to fit residues: 24.8243 Evaluate side-chains 86 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 231 TRP Chi-restraints excluded: chain C residue 302 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.1980 chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 73 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8182 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7631 Z= 0.184 Angle : 0.465 6.523 10418 Z= 0.232 Chirality : 0.038 0.134 1177 Planarity : 0.004 0.052 1265 Dihedral : 3.605 18.595 1002 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.52 % Allowed : 6.49 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.40 (0.29), residues: 926 helix: 2.51 (0.20), residues: 721 sheet: None (None), residues: 0 loop : 1.45 (0.51), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 231 HIS 0.003 0.000 HIS B 29 PHE 0.011 0.001 PHE A 288 TYR 0.008 0.001 TYR C 167 ARG 0.005 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 0.793 Fit side-chains REVERT: A 79 ARG cc_start: 0.8891 (mtp85) cc_final: 0.8585 (mtp-110) REVERT: C 153 SER cc_start: 0.8394 (m) cc_final: 0.8122 (m) REVERT: C 201 MET cc_start: 0.8554 (mmm) cc_final: 0.8275 (tpp) outliers start: 4 outliers final: 4 residues processed: 85 average time/residue: 0.2133 time to fit residues: 24.4596 Evaluate side-chains 85 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 231 TRP Chi-restraints excluded: chain C residue 302 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8192 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7631 Z= 0.205 Angle : 0.474 6.286 10418 Z= 0.237 Chirality : 0.039 0.136 1177 Planarity : 0.004 0.052 1265 Dihedral : 3.627 18.671 1002 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.52 % Allowed : 6.74 % Favored : 92.74 % 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: 3.37 (0.29), residues: 926 helix: 2.50 (0.20), residues: 721 sheet: None (None), residues: 0 loop : 1.40 (0.51), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 231 HIS 0.002 0.000 HIS A 187 PHE 0.010 0.001 PHE A 288 TYR 0.008 0.001 TYR C 167 ARG 0.005 0.000 ARG B 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.724 Fit side-chains REVERT: A 79 ARG cc_start: 0.8895 (mtp85) cc_final: 0.8583 (mtp-110) REVERT: C 153 SER cc_start: 0.8401 (m) cc_final: 0.8123 (m) REVERT: C 201 MET cc_start: 0.8553 (mmm) cc_final: 0.8277 (tpp) outliers start: 4 outliers final: 4 residues processed: 85 average time/residue: 0.2124 time to fit residues: 24.6049 Evaluate side-chains 84 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 231 TRP Chi-restraints excluded: chain C residue 302 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.118074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.095444 restraints weight = 25499.874| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.05 r_work: 0.2885 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7631 Z= 0.227 Angle : 0.482 6.224 10418 Z= 0.241 Chirality : 0.039 0.139 1177 Planarity : 0.004 0.052 1265 Dihedral : 3.660 18.790 1002 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.52 % Allowed : 6.74 % Favored : 92.74 % 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: 3.31 (0.29), residues: 926 helix: 2.46 (0.19), residues: 721 sheet: None (None), residues: 0 loop : 1.36 (0.52), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 231 HIS 0.002 0.000 HIS A 187 PHE 0.010 0.001 PHE B 197 TYR 0.008 0.001 TYR C 167 ARG 0.007 0.001 ARG B 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1940.87 seconds wall clock time: 35 minutes 21.31 seconds (2121.31 seconds total)