Starting phenix.real_space_refine on Tue Feb 13 17:29:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu0_35713/02_2024/8iu0_35713_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu0_35713/02_2024/8iu0_35713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu0_35713/02_2024/8iu0_35713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu0_35713/02_2024/8iu0_35713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu0_35713/02_2024/8iu0_35713_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu0_35713/02_2024/8iu0_35713_updated.pdb" } resolution = 2.66 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= 0.004 sd= 0.125 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 60 5.16 5 C 4863 2.51 5 N 954 2.21 5 O 1176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 7": "NH1" <-> "NH2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A GLU 65": "OE1" <-> "OE2" Residue "A ARG 151": "NH1" <-> "NH2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "B ARG 7": "NH1" <-> "NH2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B ARG 186": "NH1" <-> "NH2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "C ARG 7": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C ARG 151": "NH1" <-> "NH2" Residue "C ARG 171": "NH1" <-> "NH2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C GLU 248": "OE1" <-> "OE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C GLU 252": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7062 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2102 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 255, 2072 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} Conformer: "B" Number of residues, atoms: 255, 2072 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} bond proxies already assigned to first conformer: 2117 Chain: "A" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 252 Unusual residues: {'PLM': 4, 'PSC': 10, 'RET': 1} Classifications: {'undetermined': 15, 'water': 26} Link IDs: {None: 40} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 341 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'RET:plan-5': 1, 'PSC:plan-1': 6, 'PSC:plan-2': 6, 'PSC:plan-3': 7, 'PSC:plan-4': 7, 'PLM:plan-1': 4} Unresolved non-hydrogen planarities: 109 Chain: "B" Number of atoms: 2102 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 255, 2072 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} Conformer: "B" Number of residues, atoms: 255, 2072 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} bond proxies already assigned to first conformer: 2117 Chain: "B" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 252 Unusual residues: {'PLM': 4, 'PSC': 10, 'RET': 1} Classifications: {'undetermined': 15, 'water': 26} Link IDs: {None: 40} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 341 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'RET:plan-5': 1, 'PSC:plan-1': 6, 'PSC:plan-2': 6, 'PSC:plan-3': 7, 'PSC:plan-4': 7, 'PLM:plan-1': 4} Unresolved non-hydrogen planarities: 109 Chain: "C" Number of atoms: 2102 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 255, 2072 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} Conformer: "B" Number of residues, atoms: 255, 2072 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} bond proxies already assigned to first conformer: 2117 Chain: "C" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 252 Unusual residues: {'PLM': 4, 'PSC': 10, 'RET': 1} Classifications: {'undetermined': 15, 'water': 26} Link IDs: {None: 40} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 341 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'RET:plan-5': 1, 'PSC:plan-1': 6, 'PSC:plan-2': 6, 'PSC:plan-3': 7, 'PSC:plan-4': 7, 'PLM:plan-1': 4} Unresolved non-hydrogen planarities: 109 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N APHE A 35 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 35 " occ=0.50 residue: pdb=" N APHE A 144 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 144 " occ=0.50 residue: pdb=" N APHE B 35 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 35 " occ=0.50 residue: pdb=" N APHE B 144 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 144 " occ=0.50 residue: pdb=" N APHE C 35 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 35 " occ=0.50 residue: pdb=" N APHE C 144 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 144 " occ=0.50 Time building chain proxies: 7.07, per 1000 atoms: 1.00 Number of scatterers: 7062 At special positions: 0 Unit cell: (77.19, 77.19, 84.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 9 15.00 O 1176 8.00 N 954 7.00 C 4863 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 2.2 seconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1428 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 0 sheets defined 69.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 22 through 49 removed outlier: 3.547A pdb=" N LEU A 49 " --> pdb=" O TYR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 89 removed outlier: 4.069A pdb=" N SER A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 84 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 121 removed outlier: 5.032A pdb=" N CYS A 110 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 126 through 145 Processing helix chain 'A' and resid 149 through 176 removed outlier: 4.290A pdb=" N THR A 163 " --> pdb=" O CYS A 160 " (cutoff:3.500A) Proline residue: A 164 - end of helix removed outlier: 3.781A pdb=" N VAL A 173 " --> pdb=" O MET A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 208 removed outlier: 4.122A pdb=" N TRP A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Proline residue: A 200 - end of helix Proline residue: A 203 - end of helix removed outlier: 3.670A pdb=" N ILE A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 232 Processing helix chain 'A' and resid 234 through 251 Processing helix chain 'B' and resid 22 through 49 removed outlier: 3.548A pdb=" N LEU B 49 " --> pdb=" O TYR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 89 removed outlier: 4.069A pdb=" N SER B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS B 84 " --> pdb=" O TYR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 121 removed outlier: 5.031A pdb=" N CYS B 110 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 126 through 145 Processing helix chain 'B' and resid 149 through 176 removed outlier: 4.290A pdb=" N THR B 163 " --> pdb=" O CYS B 160 " (cutoff:3.500A) Proline residue: B 164 - end of helix removed outlier: 3.782A pdb=" N VAL B 173 " --> pdb=" O MET B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 208 removed outlier: 4.122A pdb=" N TRP B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) Proline residue: B 200 - end of helix Proline residue: B 203 - end of helix removed outlier: 3.670A pdb=" N ILE B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 232 Processing helix chain 'B' and resid 234 through 251 Processing helix chain 'C' and resid 22 through 49 removed outlier: 3.547A pdb=" N LEU C 49 " --> pdb=" O TYR C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 89 removed outlier: 4.068A pdb=" N SER C 70 " --> pdb=" O ASN C 67 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS C 84 " --> pdb=" O TYR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 121 removed outlier: 5.032A pdb=" N CYS C 110 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 126 through 145 Processing helix chain 'C' and resid 149 through 176 removed outlier: 4.290A pdb=" N THR C 163 " --> pdb=" O CYS C 160 " (cutoff:3.500A) Proline residue: C 164 - end of helix removed outlier: 3.782A pdb=" N VAL C 173 " --> pdb=" O MET C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 208 removed outlier: 4.122A pdb=" N TRP C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) Proline residue: C 200 - end of helix Proline residue: C 203 - end of helix removed outlier: 3.670A pdb=" N ILE C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 232 Processing helix chain 'C' and resid 234 through 251 390 hydrogen bonds defined for protein. 732 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: 1.63 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1226 1.33 - 1.46: 2621 1.46 - 1.59: 3260 1.59 - 1.72: 15 1.72 - 1.85: 81 Bond restraints: 7203 Sorted by residual: bond pdb=" C7 PSC C 310 " pdb=" C8 PSC C 310 " ideal model delta sigma weight residual 1.530 1.319 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C3 PSC A 311 " pdb=" C4 PSC A 311 " ideal model delta sigma weight residual 1.524 1.313 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C3 PSC B 311 " pdb=" C4 PSC B 311 " ideal model delta sigma weight residual 1.524 1.313 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C3 PSC C 311 " pdb=" C4 PSC C 311 " ideal model delta sigma weight residual 1.524 1.313 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C7 PSC A 310 " pdb=" C8 PSC A 310 " ideal model delta sigma weight residual 1.530 1.320 0.210 2.00e-02 2.50e+03 1.11e+02 ... (remaining 7198 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.65: 293 106.65 - 113.63: 3414 113.63 - 120.61: 3523 120.61 - 127.60: 2310 127.60 - 134.58: 90 Bond angle restraints: 9630 Sorted by residual: angle pdb=" C10 PSC B 310 " pdb=" C9 PSC B 310 " pdb=" C8 PSC B 310 " ideal model delta sigma weight residual 127.68 112.60 15.08 3.00e+00 1.11e-01 2.53e+01 angle pdb=" C10 PSC A 310 " pdb=" C9 PSC A 310 " pdb=" C8 PSC A 310 " ideal model delta sigma weight residual 127.68 112.60 15.08 3.00e+00 1.11e-01 2.53e+01 angle pdb=" C10 PSC C 310 " pdb=" C9 PSC C 310 " pdb=" C8 PSC C 310 " ideal model delta sigma weight residual 127.68 112.61 15.07 3.00e+00 1.11e-01 2.52e+01 angle pdb=" C10 PSC B 310 " pdb=" C11 PSC B 310 " pdb=" C12 PSC B 310 " ideal model delta sigma weight residual 111.07 126.14 -15.07 3.00e+00 1.11e-01 2.52e+01 angle pdb=" C10 PSC A 310 " pdb=" C11 PSC A 310 " pdb=" C12 PSC A 310 " ideal model delta sigma weight residual 111.07 126.12 -15.05 3.00e+00 1.11e-01 2.52e+01 ... (remaining 9625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 3708 23.98 - 47.95: 324 47.95 - 71.93: 108 71.93 - 95.90: 0 95.90 - 119.88: 3 Dihedral angle restraints: 4143 sinusoidal: 1890 harmonic: 2253 Sorted by residual: dihedral pdb=" C03 PSC C 302 " pdb=" O11 PSC C 302 " pdb=" P PSC C 302 " pdb=" O12 PSC C 302 " ideal model delta sinusoidal sigma weight residual 174.46 54.58 119.88 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C03 PSC A 302 " pdb=" O11 PSC A 302 " pdb=" P PSC A 302 " pdb=" O12 PSC A 302 " ideal model delta sinusoidal sigma weight residual 174.46 54.59 119.87 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C03 PSC B 302 " pdb=" O11 PSC B 302 " pdb=" P PSC B 302 " pdb=" O12 PSC B 302 " ideal model delta sinusoidal sigma weight residual 174.46 54.60 119.86 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 4140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 457 0.051 - 0.102: 326 0.102 - 0.153: 113 0.153 - 0.204: 31 0.204 - 0.255: 9 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA PRO A 147 " pdb=" N PRO A 147 " pdb=" C PRO A 147 " pdb=" CB PRO A 147 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA PRO C 147 " pdb=" N PRO C 147 " pdb=" C PRO C 147 " pdb=" CB PRO C 147 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA PRO B 147 " pdb=" N PRO B 147 " pdb=" C PRO B 147 " pdb=" CB PRO B 147 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 933 not shown) Planarity restraints: 1158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 PSC B 312 " -0.310 2.00e-02 2.50e+03 2.30e-01 5.28e+02 pdb=" C11 PSC B 312 " 0.102 2.00e-02 2.50e+03 pdb=" C8 PSC B 312 " -0.100 2.00e-02 2.50e+03 pdb=" C9 PSC B 312 " 0.308 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PSC A 312 " -0.310 2.00e-02 2.50e+03 2.30e-01 5.27e+02 pdb=" C11 PSC A 312 " 0.102 2.00e-02 2.50e+03 pdb=" C8 PSC A 312 " -0.099 2.00e-02 2.50e+03 pdb=" C9 PSC A 312 " 0.307 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PSC C 312 " 0.310 2.00e-02 2.50e+03 2.30e-01 5.27e+02 pdb=" C11 PSC C 312 " -0.102 2.00e-02 2.50e+03 pdb=" C8 PSC C 312 " 0.099 2.00e-02 2.50e+03 pdb=" C9 PSC C 312 " -0.307 2.00e-02 2.50e+03 ... (remaining 1155 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1594 2.79 - 3.32: 6758 3.32 - 3.84: 12297 3.84 - 4.37: 16073 4.37 - 4.90: 25247 Nonbonded interactions: 61969 Sorted by model distance: nonbonded pdb=" OH TYR A 103 " pdb=" O HOH A 401 " model vdw 2.258 2.440 nonbonded pdb=" OH TYR C 103 " pdb=" O HOH C 401 " model vdw 2.259 2.440 nonbonded pdb=" OH TYR B 103 " pdb=" O HOH B 401 " model vdw 2.259 2.440 nonbonded pdb=" NH2 ARG C 171 " pdb=" O13 PSC C 309 " model vdw 2.306 2.520 nonbonded pdb=" NH2 ARG A 171 " pdb=" O13 PSC A 309 " model vdw 2.306 2.520 ... (remaining 61964 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 34 or resid 36 through 143 or resid 145 through \ 226 or resid 228 through 260 or resid 301 through 315)) selection = (chain 'B' and (resid 6 through 34 or resid 36 through 143 or resid 145 through \ 226 or resid 228 through 260 or resid 301 through 315)) selection = (chain 'C' and (resid 6 through 34 or resid 36 through 143 or resid 145 through \ 226 or resid 228 through 260 or resid 301 through 315)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 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: 0.320 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: 0.000 Extract box with map and model: 1.450 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 26.640 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 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 : 0.014 0.211 7203 Z= 0.859 Angle : 1.596 15.084 9630 Z= 0.937 Chirality : 0.077 0.255 936 Planarity : 0.023 0.230 1158 Dihedral : 18.616 119.879 2715 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.90 % Allowed : 4.95 % Favored : 94.14 % 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: -1.94 (0.27), residues: 780 helix: -1.30 (0.19), residues: 543 sheet: None (None), residues: 0 loop : -0.76 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.011 TRP B 187 HIS 0.011 0.006 HIS C 215 PHE 0.035 0.008 PHE B 243 TYR 0.044 0.009 TYR A 150 ARG 0.016 0.003 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.768 Fit side-chains REVERT: A 207 ILE cc_start: 0.7232 (mt) cc_final: 0.7024 (mm) REVERT: A 230 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6532 (tp) REVERT: B 207 ILE cc_start: 0.7118 (mt) cc_final: 0.6911 (mm) REVERT: C 207 ILE cc_start: 0.7298 (mt) cc_final: 0.7051 (mm) outliers start: 6 outliers final: 0 residues processed: 79 average time/residue: 1.3360 time to fit residues: 111.0534 Evaluate side-chains 64 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 0.0470 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 58 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 0.0870 chunk 68 optimal weight: 0.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 7203 Z= 0.302 Angle : 1.009 14.488 9630 Z= 0.533 Chirality : 0.058 0.472 936 Planarity : 0.012 0.110 1158 Dihedral : 19.600 106.673 1334 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.19 % Favored : 93.41 % Rotamer: Outliers : 1.95 % Allowed : 7.96 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.28), residues: 780 helix: -1.46 (0.20), residues: 543 sheet: None (None), residues: 0 loop : -0.91 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.113 0.010 TRP B 138 HIS 0.019 0.004 HIS C 215 PHE 0.103 0.006 PHE C 134 TYR 0.107 0.005 TYR B 155 ARG 0.026 0.002 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.765 Fit side-chains REVERT: A 87 ASP cc_start: 0.8162 (t70) cc_final: 0.7848 (t70) REVERT: A 207 ILE cc_start: 0.7073 (mt) cc_final: 0.6850 (mm) REVERT: B 207 ILE cc_start: 0.7053 (mt) cc_final: 0.6829 (mm) REVERT: C 80 MET cc_start: 0.7905 (mtm) cc_final: 0.7572 (mtp) outliers start: 10 outliers final: 3 residues processed: 78 average time/residue: 1.1091 time to fit residues: 92.1535 Evaluate side-chains 66 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 230 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 : 0.004 0.028 7203 Z= 0.236 Angle : 0.597 6.255 9630 Z= 0.297 Chirality : 0.043 0.131 936 Planarity : 0.006 0.056 1158 Dihedral : 17.222 89.720 1332 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.65 % Allowed : 9.76 % Favored : 88.59 % 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: -0.38 (0.29), residues: 780 helix: -0.08 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.29 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 42 HIS 0.002 0.001 HIS C 172 PHE 0.017 0.002 PHE A 134 TYR 0.010 0.002 TYR A 22 ARG 0.003 0.001 ARG C 176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.740 Fit side-chains REVERT: A 87 ASP cc_start: 0.8331 (t70) cc_final: 0.7932 (t70) REVERT: A 207 ILE cc_start: 0.7054 (mt) cc_final: 0.6791 (mm) REVERT: B 80 MET cc_start: 0.7787 (mtp) cc_final: 0.7511 (mtt) REVERT: B 207 ILE cc_start: 0.7035 (mt) cc_final: 0.6801 (mm) REVERT: C 244 ARG cc_start: 0.8094 (mtm-85) cc_final: 0.7532 (mtp180) REVERT: C 248 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7262 (mt-10) outliers start: 8 outliers final: 0 residues processed: 74 average time/residue: 1.2757 time to fit residues: 99.6781 Evaluate side-chains 63 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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: 0.7552 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7203 Z= 0.168 Angle : 0.521 6.023 9630 Z= 0.259 Chirality : 0.039 0.123 936 Planarity : 0.006 0.045 1158 Dihedral : 14.669 58.284 1332 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.35 % Allowed : 9.76 % Favored : 88.89 % 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: 0.60 (0.30), residues: 780 helix: 0.64 (0.22), residues: 540 sheet: None (None), residues: 0 loop : 0.14 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 42 HIS 0.001 0.001 HIS C 215 PHE 0.016 0.001 PHE A 134 TYR 0.009 0.001 TYR A 81 ARG 0.003 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.709 Fit side-chains REVERT: A 207 ILE cc_start: 0.6895 (mt) cc_final: 0.6681 (mm) REVERT: B 80 MET cc_start: 0.7929 (mtp) cc_final: 0.7682 (mtt) REVERT: B 81 TYR cc_start: 0.8591 (m-80) cc_final: 0.8242 (m-80) REVERT: B 207 ILE cc_start: 0.6912 (mt) cc_final: 0.6683 (mm) REVERT: C 244 ARG cc_start: 0.8139 (mtm-85) cc_final: 0.7440 (mtm-85) outliers start: 6 outliers final: 2 residues processed: 65 average time/residue: 1.2601 time to fit residues: 86.6458 Evaluate side-chains 59 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain C residue 16 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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: 0.7589 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7203 Z= 0.214 Angle : 0.561 6.106 9630 Z= 0.275 Chirality : 0.041 0.131 936 Planarity : 0.006 0.039 1158 Dihedral : 14.241 59.172 1332 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.50 % Allowed : 9.31 % Favored : 89.19 % 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: 0.71 (0.29), residues: 780 helix: 0.72 (0.21), residues: 540 sheet: None (None), residues: 0 loop : 0.18 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 42 HIS 0.001 0.001 HIS C 125 PHE 0.016 0.002 PHE A 134 TYR 0.010 0.001 TYR C 81 ARG 0.003 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.793 Fit side-chains REVERT: A 87 ASP cc_start: 0.8293 (t70) cc_final: 0.7863 (t70) REVERT: B 80 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7721 (mtt) REVERT: C 244 ARG cc_start: 0.8169 (mtm-85) cc_final: 0.7487 (mtm-85) outliers start: 7 outliers final: 3 residues processed: 63 average time/residue: 1.3101 time to fit residues: 87.4088 Evaluate side-chains 58 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 16 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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: 0.7576 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7203 Z= 0.193 Angle : 0.538 6.392 9630 Z= 0.264 Chirality : 0.040 0.127 936 Planarity : 0.006 0.038 1158 Dihedral : 13.418 59.871 1332 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.05 % Allowed : 9.91 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.29), residues: 780 helix: 0.86 (0.21), residues: 540 sheet: None (None), residues: 0 loop : 0.20 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 42 HIS 0.001 0.001 HIS C 215 PHE 0.016 0.001 PHE A 134 TYR 0.009 0.001 TYR C 81 ARG 0.002 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.791 Fit side-chains REVERT: A 87 ASP cc_start: 0.8286 (t70) cc_final: 0.7835 (t70) REVERT: B 80 MET cc_start: 0.8089 (mtp) cc_final: 0.7774 (mtt) REVERT: C 244 ARG cc_start: 0.8132 (mtm-85) cc_final: 0.7450 (mtm-85) outliers start: 4 outliers final: 2 residues processed: 61 average time/residue: 1.2941 time to fit residues: 83.6090 Evaluate side-chains 56 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain C residue 16 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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: 0.7578 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7203 Z= 0.191 Angle : 0.537 6.590 9630 Z= 0.263 Chirality : 0.040 0.128 936 Planarity : 0.006 0.039 1158 Dihedral : 12.988 58.163 1332 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.05 % Allowed : 10.21 % Favored : 88.74 % 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: 0.94 (0.29), residues: 780 helix: 0.91 (0.21), residues: 540 sheet: None (None), residues: 0 loop : 0.20 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 42 HIS 0.002 0.001 HIS C 215 PHE 0.016 0.001 PHE A 134 TYR 0.010 0.001 TYR C 81 ARG 0.002 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.765 Fit side-chains REVERT: A 87 ASP cc_start: 0.8282 (t70) cc_final: 0.7824 (t70) REVERT: B 80 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7776 (mtt) REVERT: C 244 ARG cc_start: 0.8122 (mtm-85) cc_final: 0.7444 (mtm-85) outliers start: 4 outliers final: 2 residues processed: 59 average time/residue: 1.3239 time to fit residues: 82.5407 Evaluate side-chains 58 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 16 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 35 optimal weight: 0.0970 chunk 6 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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: 0.7578 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7203 Z= 0.192 Angle : 0.535 6.754 9630 Z= 0.262 Chirality : 0.040 0.128 936 Planarity : 0.006 0.039 1158 Dihedral : 12.831 59.846 1332 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.20 % Allowed : 10.21 % Favored : 88.59 % 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: 0.96 (0.29), residues: 780 helix: 0.93 (0.21), residues: 540 sheet: None (None), residues: 0 loop : 0.21 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 42 HIS 0.001 0.001 HIS C 215 PHE 0.015 0.001 PHE A 134 TYR 0.009 0.001 TYR C 81 ARG 0.002 0.000 ARG C 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.712 Fit side-chains REVERT: B 80 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7788 (mtt) REVERT: C 244 ARG cc_start: 0.8134 (mtm-85) cc_final: 0.7449 (mtm-85) outliers start: 5 outliers final: 2 residues processed: 57 average time/residue: 1.2921 time to fit residues: 78.0500 Evaluate side-chains 58 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 16 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 60 optimal weight: 0.0980 chunk 63 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- 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: 0.7596 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7203 Z= 0.229 Angle : 0.567 6.559 9630 Z= 0.276 Chirality : 0.041 0.131 936 Planarity : 0.006 0.039 1158 Dihedral : 13.180 59.405 1332 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.05 % Allowed : 10.66 % Favored : 88.29 % 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: 0.82 (0.29), residues: 780 helix: 0.81 (0.21), residues: 543 sheet: None (None), residues: 0 loop : 0.19 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 102 HIS 0.002 0.001 HIS C 125 PHE 0.015 0.002 PHE A 134 TYR 0.011 0.001 TYR C 81 ARG 0.003 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.764 Fit side-chains REVERT: A 87 ASP cc_start: 0.8291 (t70) cc_final: 0.7857 (t70) REVERT: B 80 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7759 (mtt) REVERT: C 244 ARG cc_start: 0.8181 (mtm-85) cc_final: 0.7485 (mtm-85) outliers start: 4 outliers final: 2 residues processed: 61 average time/residue: 1.3267 time to fit residues: 85.4693 Evaluate side-chains 60 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 16 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.7551 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7203 Z= 0.151 Angle : 0.500 6.583 9630 Z= 0.247 Chirality : 0.038 0.120 936 Planarity : 0.006 0.040 1158 Dihedral : 12.271 58.568 1332 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.90 % Allowed : 10.66 % Favored : 88.44 % 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: 1.10 (0.30), residues: 780 helix: 1.02 (0.22), residues: 540 sheet: None (None), residues: 0 loop : 0.30 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 102 HIS 0.001 0.001 HIS C 125 PHE 0.015 0.001 PHE A 134 TYR 0.008 0.001 TYR C 81 ARG 0.001 0.000 ARG C 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.718 Fit side-chains REVERT: B 80 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7806 (mtt) REVERT: C 244 ARG cc_start: 0.8133 (mtm-85) cc_final: 0.7468 (mtm-85) outliers start: 3 outliers final: 2 residues processed: 59 average time/residue: 1.3340 time to fit residues: 83.1456 Evaluate side-chains 58 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 16 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3426 r_free = 0.3426 target = 0.124471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.101964 restraints weight = 31273.793| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.23 r_work: 0.3053 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7203 Z= 0.215 Angle : 0.553 6.502 9630 Z= 0.270 Chirality : 0.041 0.130 936 Planarity : 0.006 0.039 1158 Dihedral : 12.711 59.319 1332 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.20 % Allowed : 10.21 % Favored : 88.59 % 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: 0.98 (0.29), residues: 780 helix: 0.93 (0.21), residues: 540 sheet: None (None), residues: 0 loop : 0.25 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 102 HIS 0.001 0.001 HIS C 215 PHE 0.015 0.001 PHE A 134 TYR 0.011 0.001 TYR C 81 ARG 0.003 0.000 ARG A 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2159.82 seconds wall clock time: 39 minutes 35.93 seconds (2375.93 seconds total)