Starting phenix.real_space_refine on Tue Jun 25 08:37:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi2_43246/06_2024/8vi2_43246.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi2_43246/06_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_43246/06_2024/8vi2_43246.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi2_43246/06_2024/8vi2_43246.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi2_43246/06_2024/8vi2_43246.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vi2_43246/06_2024/8vi2_43246.pdb" } 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 10.28, per 1000 atoms: 1.39 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: 3.55 Conformation dependent library (CDL) restraints added in 2.9 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: 0.77 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: 2.12 Time building geometry restraints manager: 3.80 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 2.440 nonbonded pdb=" O THR C 121 " pdb=" OG SER C 125 " model vdw 2.053 2.440 nonbonded pdb=" O THR A 121 " pdb=" OG SER A 125 " model vdw 2.063 2.440 nonbonded pdb=" OH TYR B 215 " pdb=" OD2 ASP B 224 " model vdw 2.095 2.440 nonbonded pdb=" OH TYR C 13 " pdb=" O PHE C 311 " model vdw 2.113 2.440 ... (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 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: 4.400 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: 17.410 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 32.680 Find NCS groups from input model: 0.500 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.820 ------------------------------------------------------------------------------- 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 : 0.795 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1871 time to fit residues: 18.8496 Evaluate side-chains 66 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.9980 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS A 276 HIS B 163 HIS B 276 HIS C 276 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7631 Z= 0.247 Angle : 0.509 5.913 10418 Z= 0.261 Chirality : 0.041 0.142 1177 Planarity : 0.004 0.054 1265 Dihedral : 3.663 19.613 1002 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.39 % Allowed : 3.50 % Favored : 96.11 % 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: 926 helix: 1.92 (0.19), residues: 725 sheet: None (None), residues: 0 loop : 1.92 (0.52), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 231 HIS 0.002 0.001 HIS A 29 PHE 0.012 0.001 PHE C 7 TYR 0.018 0.001 TYR C 167 ARG 0.003 0.001 ARG A 198 *********************** 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 78 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.696 Fit side-chains REVERT: A 79 ARG cc_start: 0.8868 (mtp85) cc_final: 0.8563 (mtp-110) REVERT: C 278 ASN cc_start: 0.8684 (t0) cc_final: 0.8472 (t0) outliers start: 3 outliers final: 2 residues processed: 75 average time/residue: 0.2078 time to fit residues: 21.2637 Evaluate side-chains 74 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL 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: 0.7980 chunk 25 optimal weight: 0.3980 chunk 68 optimal weight: 0.5980 chunk 55 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.8156 moved from start: 0.1463 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= 0.189 Angle : 0.472 6.225 10418 Z= 0.239 Chirality : 0.039 0.132 1177 Planarity : 0.004 0.055 1265 Dihedral : 3.592 19.255 1002 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.39 % Allowed : 4.28 % Favored : 95.33 % 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: 3.47 (0.29), residues: 926 helix: 2.54 (0.20), residues: 705 sheet: None (None), residues: 0 loop : 1.66 (0.50), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 231 HIS 0.004 0.001 HIS B 29 PHE 0.010 0.001 PHE A 288 TYR 0.013 0.001 TYR C 167 ARG 0.005 0.000 ARG B 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 79 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.782 Fit side-chains REVERT: A 79 ARG cc_start: 0.8875 (mtp85) cc_final: 0.8583 (mtp-110) REVERT: C 278 ASN cc_start: 0.8735 (t0) cc_final: 0.8448 (t0) outliers start: 3 outliers final: 3 residues processed: 79 average time/residue: 0.2220 time to fit residues: 23.3784 Evaluate side-chains 73 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 49 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 HIS C 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7631 Z= 0.177 Angle : 0.458 6.637 10418 Z= 0.230 Chirality : 0.039 0.135 1177 Planarity : 0.004 0.051 1265 Dihedral : 3.553 19.110 1002 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.52 % Allowed : 5.32 % Favored : 94.16 % 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: 3.54 (0.29), residues: 926 helix: 2.59 (0.20), residues: 704 sheet: None (None), residues: 0 loop : 1.71 (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 0.010 0.001 PHE A 288 TYR 0.011 0.001 TYR C 167 ARG 0.005 0.000 ARG B 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 82 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.772 Fit side-chains REVERT: A 79 ARG cc_start: 0.8885 (mtp85) cc_final: 0.8583 (mtp-110) REVERT: C 278 ASN cc_start: 0.8741 (t0) cc_final: 0.8467 (t0) outliers start: 4 outliers final: 3 residues processed: 81 average time/residue: 0.2097 time to fit residues: 22.8595 Evaluate side-chains 76 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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: 0.6980 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8191 moved from start: 0.1779 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= 0.211 Angle : 0.470 5.643 10418 Z= 0.235 Chirality : 0.039 0.134 1177 Planarity : 0.004 0.052 1265 Dihedral : 3.598 19.170 1002 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.52 % Allowed : 5.45 % 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: 3.43 (0.29), residues: 926 helix: 2.51 (0.19), residues: 706 sheet: None (None), residues: 0 loop : 1.64 (0.51), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 231 HIS 0.002 0.000 HIS A 187 PHE 0.009 0.001 PHE A 288 TYR 0.009 0.001 TYR C 167 ARG 0.005 0.000 ARG C 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 84 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.829 Fit side-chains REVERT: A 79 ARG cc_start: 0.8890 (mtp85) cc_final: 0.8577 (mtp-110) REVERT: C 278 ASN cc_start: 0.8769 (t0) cc_final: 0.8515 (t0) outliers start: 4 outliers final: 4 residues processed: 83 average time/residue: 0.2175 time to fit residues: 24.4681 Evaluate side-chains 80 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 231 TRP 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: 0.5980 chunk 21 optimal weight: 0.9990 chunk 87 optimal weight: 0.3980 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1867 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= 0.192 Angle : 0.459 6.766 10418 Z= 0.229 Chirality : 0.038 0.133 1177 Planarity : 0.004 0.052 1265 Dihedral : 3.576 18.925 1002 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.52 % Allowed : 6.10 % Favored : 93.39 % 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: 2.47 (0.19), residues: 718 sheet: None (None), residues: 0 loop : 1.51 (0.52), residues: 208 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 0.010 0.001 PHE A 288 TYR 0.008 0.001 TYR A 59 ARG 0.005 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 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 82 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.721 Fit side-chains REVERT: A 79 ARG cc_start: 0.8883 (mtp85) cc_final: 0.8575 (mtp-110) REVERT: C 201 MET cc_start: 0.8521 (mmm) cc_final: 0.8305 (tpp) REVERT: C 278 ASN cc_start: 0.8763 (t0) cc_final: 0.8543 (t0) outliers start: 4 outliers final: 4 residues processed: 82 average time/residue: 0.2113 time to fit residues: 23.2659 Evaluate side-chains 80 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 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: 2.9990 chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 0.1980 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 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: 0.8190 moved from start: 0.1906 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= 0.202 Angle : 0.461 5.600 10418 Z= 0.231 Chirality : 0.039 0.132 1177 Planarity : 0.004 0.052 1265 Dihedral : 3.581 18.888 1002 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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: 3.35 (0.29), residues: 926 helix: 2.47 (0.19), residues: 718 sheet: None (None), residues: 0 loop : 1.49 (0.52), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 231 HIS 0.002 0.000 HIS B 29 PHE 0.009 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 85 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.828 Fit side-chains REVERT: A 79 ARG cc_start: 0.8888 (mtp85) cc_final: 0.8575 (mtp-110) REVERT: C 201 MET cc_start: 0.8524 (mmm) cc_final: 0.8313 (tpp) REVERT: C 278 ASN cc_start: 0.8760 (t0) cc_final: 0.8557 (t0) outliers start: 4 outliers final: 4 residues processed: 84 average time/residue: 0.2127 time to fit residues: 24.1573 Evaluate side-chains 81 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 231 TRP 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: 0.8980 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 68 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1949 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= 0.186 Angle : 0.462 7.411 10418 Z= 0.229 Chirality : 0.038 0.131 1177 Planarity : 0.004 0.052 1265 Dihedral : 3.560 18.703 1002 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.52 % Allowed : 5.97 % Favored : 93.51 % 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: 2.49 (0.19), residues: 721 sheet: None (None), residues: 0 loop : 1.51 (0.51), 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 0.009 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 82 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.751 Fit side-chains REVERT: A 79 ARG cc_start: 0.8888 (mtp85) cc_final: 0.8577 (mtp-110) REVERT: C 201 MET cc_start: 0.8516 (mmm) cc_final: 0.8301 (tpp) outliers start: 4 outliers final: 4 residues processed: 82 average time/residue: 0.2059 time to fit residues: 22.9237 Evaluate side-chains 79 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain C residue 231 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 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: 0.8186 moved from start: 0.1974 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= 0.195 Angle : 0.462 6.221 10418 Z= 0.231 Chirality : 0.038 0.131 1177 Planarity : 0.004 0.052 1265 Dihedral : 3.563 18.773 1002 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.52 % Allowed : 5.97 % Favored : 93.51 % 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: 3.43 (0.29), residues: 926 helix: 2.54 (0.19), residues: 716 sheet: None (None), residues: 0 loop : 1.45 (0.51), residues: 210 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 0.009 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 85 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.747 Fit side-chains REVERT: A 79 ARG cc_start: 0.8888 (mtp85) cc_final: 0.8572 (mtp-110) REVERT: C 201 MET cc_start: 0.8520 (mmm) cc_final: 0.8311 (tpp) outliers start: 4 outliers final: 4 residues processed: 85 average time/residue: 0.2085 time to fit residues: 23.8963 Evaluate side-chains 83 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 231 TRP 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: 0.5980 chunk 89 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 55 optimal weight: 0.0570 chunk 43 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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: 0.8175 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7631 Z= 0.179 Angle : 0.457 6.593 10418 Z= 0.227 Chirality : 0.038 0.130 1177 Planarity : 0.004 0.052 1265 Dihedral : 3.536 18.689 1002 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.52 % Allowed : 6.23 % Favored : 93.26 % 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: 3.48 (0.29), residues: 926 helix: 2.55 (0.19), residues: 721 sheet: None (None), residues: 0 loop : 1.54 (0.51), 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 0.009 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 84 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.801 Fit side-chains REVERT: A 79 ARG cc_start: 0.8881 (mtp85) cc_final: 0.8569 (mtp-110) REVERT: C 201 MET cc_start: 0.8506 (mmm) cc_final: 0.8305 (tpp) outliers start: 4 outliers final: 4 residues processed: 84 average time/residue: 0.2151 time to fit residues: 24.2013 Evaluate side-chains 84 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 231 TRP 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: 0.7980 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 62 optimal weight: 0.0970 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.116567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.095139 restraints weight = 25484.855| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.92 r_work: 0.2907 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2023 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= 0.202 Angle : 0.466 6.286 10418 Z= 0.232 Chirality : 0.038 0.132 1177 Planarity : 0.004 0.051 1265 Dihedral : 3.556 18.731 1002 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.52 % Allowed : 6.36 % Favored : 93.13 % 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: 3.43 (0.29), residues: 926 helix: 2.54 (0.19), residues: 716 sheet: None (None), residues: 0 loop : 1.46 (0.51), residues: 210 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 0.008 0.001 PHE A 288 TYR 0.007 0.001 TYR A 59 ARG 0.005 0.000 ARG B 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1960.96 seconds wall clock time: 35 minutes 36.64 seconds (2136.64 seconds total)