Starting phenix.real_space_refine (version: dev) on Thu May 12 18:56:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfk_25091/05_2022/7sfk_25091_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfk_25091/05_2022/7sfk_25091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfk_25091/05_2022/7sfk_25091.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfk_25091/05_2022/7sfk_25091.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfk_25091/05_2022/7sfk_25091_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfk_25091/05_2022/7sfk_25091_updated.pdb" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.202 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 126": "OD1" <-> "OD2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 126": "OD1" <-> "OD2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B ASP 241": "OD1" <-> "OD2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 126": "OD1" <-> "OD2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C ASP 241": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 7419 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2299 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2299 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2299 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 155 Unusual residues: {'PEE': 7, 'RET': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'RET:plan-5': 1, 'PEE:plan-1': 5, 'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 146 Unusual residues: {'PEE': 6, 'RET': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'RET:plan-5': 1, 'PEE:plan-1': 4, 'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 164 Unusual residues: {'PEE': 8, 'RET': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'RET:plan-5': 1, 'PEE:plan-1': 6, 'PEE:plan-2': 4} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Time building chain proxies: 4.80, per 1000 atoms: 0.65 Number of scatterers: 7419 At special positions: 0 Unit cell: (78.453, 79.59, 88.686, 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 48 16.00 P 3 15.00 O 1299 8.00 N 1098 7.00 C 4971 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: 3.21 Conformation dependent library (CDL) restraints added in 999.7 milliseconds 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 0 sheets defined 71.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 18 through 20 No H-bonds generated for 'chain 'A' and resid 18 through 20' Processing helix chain 'A' and resid 27 through 52 Processing helix chain 'A' and resid 64 through 67 No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 69 through 94 removed outlier: 4.477A pdb=" N ALA A 74 " --> pdb=" O GLN A 71 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY A 87 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 131 Proline residue: A 121 - end of helix removed outlier: 3.610A pdb=" N GLN A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 157 Processing helix chain 'A' and resid 161 through 199 removed outlier: 5.166A pdb=" N ASN A 165 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 166 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 232 removed outlier: 3.736A pdb=" N HIS A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL A 211 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TRP A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ILE A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU A 225 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N PHE A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Proline residue: A 227 - end of helix Processing helix chain 'A' and resid 242 through 268 removed outlier: 3.601A pdb=" N GLU A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.705A pdb=" N GLY A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N HIS A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 20 No H-bonds generated for 'chain 'B' and resid 18 through 20' Processing helix chain 'B' and resid 27 through 52 Processing helix chain 'B' and resid 64 through 67 No H-bonds generated for 'chain 'B' and resid 64 through 67' Processing helix chain 'B' and resid 69 through 94 removed outlier: 4.477A pdb=" N ALA B 74 " --> pdb=" O GLN B 71 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY B 87 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 131 Proline residue: B 121 - end of helix removed outlier: 3.610A pdb=" N GLN B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 157 Processing helix chain 'B' and resid 161 through 199 removed outlier: 5.166A pdb=" N ASN B 165 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY B 166 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 232 removed outlier: 3.736A pdb=" N HIS B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL B 211 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N TRP B 223 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ILE B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU B 225 " --> pdb=" O MET B 221 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N PHE B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Proline residue: B 227 - end of helix Processing helix chain 'B' and resid 242 through 268 removed outlier: 3.600A pdb=" N GLU B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR B 260 " --> pdb=" O ALA B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.706A pdb=" N GLY B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N HIS B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 20 No H-bonds generated for 'chain 'C' and resid 18 through 20' Processing helix chain 'C' and resid 27 through 52 Processing helix chain 'C' and resid 64 through 67 No H-bonds generated for 'chain 'C' and resid 64 through 67' Processing helix chain 'C' and resid 69 through 94 removed outlier: 4.477A pdb=" N ALA C 74 " --> pdb=" O GLN C 71 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY C 87 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 131 Proline residue: C 121 - end of helix removed outlier: 3.610A pdb=" N GLN C 130 " --> pdb=" O ASP C 126 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 157 Processing helix chain 'C' and resid 161 through 199 removed outlier: 5.166A pdb=" N ASN C 165 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY C 166 " --> pdb=" O LEU C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 232 removed outlier: 3.736A pdb=" N HIS C 210 " --> pdb=" O GLU C 206 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL C 211 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N TRP C 223 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ILE C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU C 225 " --> pdb=" O MET C 221 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N PHE C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 242 through 268 removed outlier: 3.600A pdb=" N GLU C 246 " --> pdb=" O ASP C 242 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 removed outlier: 3.706A pdb=" N GLY C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N HIS C 284 " --> pdb=" O GLU C 280 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 765 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: 2.02 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2059 1.34 - 1.45: 1517 1.45 - 1.57: 3918 1.57 - 1.69: 3 1.69 - 1.81: 75 Bond restraints: 7572 Sorted by residual: bond pdb=" C30 PEE B 404 " pdb=" O5 PEE B 404 " ideal model delta sigma weight residual 1.206 1.353 -0.147 2.00e-02 2.50e+03 5.40e+01 bond pdb=" C30 PEE A 404 " pdb=" O5 PEE A 404 " ideal model delta sigma weight residual 1.206 1.353 -0.147 2.00e-02 2.50e+03 5.40e+01 bond pdb=" C30 PEE C 405 " pdb=" O5 PEE C 405 " ideal model delta sigma weight residual 1.206 1.352 -0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" C30 PEE B 402 " pdb=" O5 PEE B 402 " ideal model delta sigma weight residual 1.206 1.352 -0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" C30 PEE C 403 " pdb=" O5 PEE C 403 " ideal model delta sigma weight residual 1.206 1.352 -0.146 2.00e-02 2.50e+03 5.33e+01 ... (remaining 7567 not shown) Histogram of bond angle deviations from ideal: 98.71 - 105.77: 107 105.77 - 112.84: 3832 112.84 - 119.91: 2642 119.91 - 126.98: 3459 126.98 - 134.04: 127 Bond angle restraints: 10167 Sorted by residual: angle pdb=" C11 PEE C 402 " pdb=" C10 PEE C 402 " pdb=" O2 PEE C 402 " ideal model delta sigma weight residual 111.70 123.94 -12.24 3.00e+00 1.11e-01 1.66e+01 angle pdb=" C11 PEE B 401 " pdb=" C10 PEE B 401 " pdb=" O2 PEE B 401 " ideal model delta sigma weight residual 111.70 123.93 -12.23 3.00e+00 1.11e-01 1.66e+01 angle pdb=" C11 PEE A 401 " pdb=" C10 PEE A 401 " pdb=" O2 PEE A 401 " ideal model delta sigma weight residual 111.70 123.92 -12.22 3.00e+00 1.11e-01 1.66e+01 angle pdb=" C31 PEE B 404 " pdb=" C30 PEE B 404 " pdb=" O3 PEE B 404 " ideal model delta sigma weight residual 111.87 123.95 -12.08 3.00e+00 1.11e-01 1.62e+01 angle pdb=" C31 PEE A 404 " pdb=" C30 PEE A 404 " pdb=" O3 PEE A 404 " ideal model delta sigma weight residual 111.87 123.91 -12.04 3.00e+00 1.11e-01 1.61e+01 ... (remaining 10162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 4176 35.68 - 71.36: 90 71.36 - 107.04: 12 107.04 - 142.72: 6 142.72 - 178.40: 6 Dihedral angle restraints: 4290 sinusoidal: 1815 harmonic: 2475 Sorted by residual: dihedral pdb=" C32 PEE C 404 " pdb=" C30 PEE C 404 " pdb=" C31 PEE C 404 " pdb=" O3 PEE C 404 " ideal model delta sinusoidal sigma weight residual 161.16 -20.44 -178.40 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C32 PEE B 403 " pdb=" C30 PEE B 403 " pdb=" C31 PEE B 403 " pdb=" O3 PEE B 403 " ideal model delta sinusoidal sigma weight residual 161.16 -20.49 -178.35 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C32 PEE A 403 " pdb=" C30 PEE A 403 " pdb=" C31 PEE A 403 " pdb=" O3 PEE A 403 " ideal model delta sinusoidal sigma weight residual 161.16 -20.54 -178.30 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 4287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 633 0.033 - 0.065: 282 0.065 - 0.098: 78 0.098 - 0.130: 15 0.130 - 0.163: 3 Chirality restraints: 1011 Sorted by residual: chirality pdb=" C2 PEE A 406 " pdb=" C1 PEE A 406 " pdb=" C3 PEE A 406 " pdb=" O2 PEE A 406 " both_signs ideal model delta sigma weight residual False -2.33 -2.49 0.16 2.00e-01 2.50e+01 6.63e-01 chirality pdb=" C2 PEE B 406 " pdb=" C1 PEE B 406 " pdb=" C3 PEE B 406 " pdb=" O2 PEE B 406 " both_signs ideal model delta sigma weight residual False -2.33 -2.49 0.16 2.00e-01 2.50e+01 6.52e-01 chirality pdb=" C2 PEE C 408 " pdb=" C1 PEE C 408 " pdb=" C3 PEE C 408 " pdb=" O2 PEE C 408 " both_signs ideal model delta sigma weight residual False -2.33 -2.48 0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 1008 not shown) Planarity restraints: 1242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 160 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO B 161 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 161 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 161 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 160 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO A 161 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 160 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO C 161 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 161 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 161 " -0.028 5.00e-02 4.00e+02 ... (remaining 1239 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1880 2.79 - 3.32: 6680 3.32 - 3.85: 12450 3.85 - 4.37: 15216 4.37 - 4.90: 26101 Nonbonded interactions: 62327 Sorted by model distance: nonbonded pdb=" O GLY C 107 " pdb=" O HOH C 501 " model vdw 2.265 2.440 nonbonded pdb=" O GLY B 107 " pdb=" O HOH B 501 " model vdw 2.273 2.440 nonbonded pdb=" O GLY A 107 " pdb=" O HOH A 501 " model vdw 2.276 2.440 nonbonded pdb=" OD1 ASN A 110 " pdb=" O HOH A 502 " model vdw 2.321 2.440 nonbonded pdb=" OD1 ASN B 110 " pdb=" O HOH B 502 " model vdw 2.323 2.440 ... (remaining 62322 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 2 through 285 or (resid 403 through 404 and (name C30 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42 or name O3 or name O \ 5 )) or (resid 405 and (name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41 or name C42)) or (resid 406 and (name C36 or name C37 or name C38 o \ r name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name C \ 45 or name C46 or name C47)))) selection = (chain 'B' and (resid 2 through 285 or (resid 403 through 404 and (name C30 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42 or name O3 or name O \ 5 )) or (resid 405 and (name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41 or name C42)) or (resid 406 and (name C36 or name C37 or name C38 o \ r name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name C \ 45 or name C46 or name C47)))) selection = (chain 'C' and (resid 2 through 285 or (resid 403 through 404 and (name C30 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42 or name O3 or name O \ 5 )) or (resid 405 and (name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41 or name C42)) or resid 406)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 48 5.16 5 C 4971 2.51 5 N 1098 2.21 5 O 1299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 0.430 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: 2.950 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.070 Process input model: 23.260 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 39.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 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 : 0.008 0.147 7572 Z= 0.489 Angle : 0.966 12.239 10167 Z= 0.401 Chirality : 0.039 0.163 1011 Planarity : 0.005 0.050 1242 Dihedral : 18.019 178.399 2724 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.43 % 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: 2.37 (0.28), residues: 843 helix: 1.80 (0.20), residues: 576 sheet: None (None), residues: 0 loop : 1.31 (0.38), residues: 267 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.769 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 101 average time/residue: 0.9248 time to fit residues: 100.3427 Evaluate side-chains 79 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.793 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.9726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 76 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN C 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 7572 Z= 0.172 Angle : 0.476 4.836 10167 Z= 0.271 Chirality : 0.037 0.118 1011 Planarity : 0.007 0.046 1242 Dihedral : 15.033 137.184 1269 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 0.85 % 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: 1.86 (0.27), residues: 843 helix: 1.41 (0.21), residues: 576 sheet: None (None), residues: 0 loop : 1.11 (0.35), residues: 267 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.822 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 90 average time/residue: 0.9870 time to fit residues: 95.4135 Evaluate side-chains 86 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.759 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 1.0339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN C 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 7572 Z= 0.230 Angle : 0.507 5.178 10167 Z= 0.282 Chirality : 0.039 0.120 1011 Planarity : 0.007 0.050 1242 Dihedral : 13.536 115.332 1269 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.27), residues: 843 helix: 0.93 (0.21), residues: 573 sheet: None (None), residues: 0 loop : 1.02 (0.34), residues: 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.812 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 92 average time/residue: 0.9919 time to fit residues: 97.8152 Evaluate side-chains 88 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.795 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1094 time to fit residues: 1.1275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 76 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN C 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 7572 Z= 0.158 Angle : 0.447 5.270 10167 Z= 0.252 Chirality : 0.037 0.119 1011 Planarity : 0.006 0.049 1242 Dihedral : 11.936 114.197 1269 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 0.57 % 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: 1.33 (0.28), residues: 843 helix: 0.92 (0.21), residues: 576 sheet: None (None), residues: 0 loop : 1.15 (0.35), residues: 267 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.792 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 91 average time/residue: 1.0423 time to fit residues: 101.4861 Evaluate side-chains 86 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.784 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1270 time to fit residues: 1.2293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 56 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN C 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 7572 Z= 0.175 Angle : 0.459 5.365 10167 Z= 0.257 Chirality : 0.037 0.120 1011 Planarity : 0.006 0.050 1242 Dihedral : 11.837 114.690 1269 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 0.57 % 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: 1.25 (0.28), residues: 843 helix: 0.85 (0.21), residues: 576 sheet: None (None), residues: 0 loop : 1.14 (0.35), residues: 267 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.861 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 92 average time/residue: 1.0488 time to fit residues: 103.0295 Evaluate side-chains 88 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.752 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1184 time to fit residues: 1.2714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 81 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 GLN C 9 GLN C 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7572 Z= 0.192 Angle : 0.472 5.491 10167 Z= 0.263 Chirality : 0.038 0.121 1011 Planarity : 0.006 0.050 1242 Dihedral : 11.953 114.683 1269 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.57 % 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: 1.19 (0.28), residues: 843 helix: 0.81 (0.21), residues: 576 sheet: None (None), residues: 0 loop : 1.12 (0.35), residues: 267 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.784 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 90 average time/residue: 1.0631 time to fit residues: 102.1001 Evaluate side-chains 86 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.805 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.2004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 68 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN C 9 GLN C 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7572 Z= 0.192 Angle : 0.474 5.486 10167 Z= 0.264 Chirality : 0.038 0.122 1011 Planarity : 0.007 0.051 1242 Dihedral : 11.984 114.648 1269 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.43 % 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: 1.18 (0.28), residues: 843 helix: 0.80 (0.21), residues: 576 sheet: None (None), residues: 0 loop : 1.11 (0.35), residues: 267 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 0.852 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 90 average time/residue: 0.9988 time to fit residues: 96.2728 Evaluate side-chains 86 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.0619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.0370 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 78 ASN C 9 GLN C 68 GLN C 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 7572 Z= 0.300 Angle : 0.549 5.377 10167 Z= 0.300 Chirality : 0.041 0.127 1011 Planarity : 0.007 0.052 1242 Dihedral : 13.092 115.226 1269 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 0.71 % 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 (0.27), residues: 843 helix: 0.58 (0.21), residues: 573 sheet: None (None), residues: 0 loop : 0.97 (0.35), residues: 270 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.775 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 94 average time/residue: 1.0397 time to fit residues: 104.4143 Evaluate side-chains 91 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 0.823 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 1.2070 time to fit residues: 2.3492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN C 9 GLN C 68 GLN C 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 7572 Z= 0.268 Angle : 0.528 5.248 10167 Z= 0.291 Chirality : 0.040 0.127 1011 Planarity : 0.007 0.051 1242 Dihedral : 12.969 114.957 1269 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.43 % 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: 0.81 (0.27), residues: 843 helix: 0.52 (0.21), residues: 573 sheet: None (None), residues: 0 loop : 0.95 (0.36), residues: 270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.792 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 94 average time/residue: 0.9783 time to fit residues: 98.6037 Evaluate side-chains 90 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.778 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.0281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN C 9 GLN C 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 7572 Z= 0.181 Angle : 0.471 5.320 10167 Z= 0.264 Chirality : 0.037 0.123 1011 Planarity : 0.007 0.050 1242 Dihedral : 12.174 114.405 1269 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.43 % 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: 1.01 (0.28), residues: 843 helix: 0.64 (0.21), residues: 576 sheet: None (None), residues: 0 loop : 1.14 (0.36), residues: 267 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.839 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 94 average time/residue: 0.9957 time to fit residues: 100.5116 Evaluate side-chains 92 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.813 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 1 average time/residue: 0.1154 time to fit residues: 1.2193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 66 optimal weight: 0.0070 chunk 27 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 48 optimal weight: 10.0000 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN C 9 GLN C 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.116888 restraints weight = 7068.226| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.16 r_work: 0.3203 rms_B_bonded: 1.02 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 1.07 restraints_weight: 0.2500 r_work: 0.3171 rms_B_bonded: 1.19 restraints_weight: 0.1250 r_work: 0.3152 rms_B_bonded: 1.39 restraints_weight: 0.0625 r_work: 0.3129 rms_B_bonded: 1.65 restraints_weight: 0.0312 r_work: 0.3103 rms_B_bonded: 2.00 restraints_weight: 0.0156 r_work: 0.3071 rms_B_bonded: 2.45 restraints_weight: 0.0078 r_work: 0.3033 rms_B_bonded: 3.03 restraints_weight: 0.0039 r_work: 0.2987 rms_B_bonded: 3.77 restraints_weight: 0.0020 r_work: 0.2931 rms_B_bonded: 4.71 restraints_weight: 0.0010 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 7572 Z= 0.139 Angle : 0.436 5.575 10167 Z= 0.247 Chirality : 0.036 0.120 1011 Planarity : 0.006 0.050 1242 Dihedral : 11.476 113.673 1269 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 0.43 % 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: 1.19 (0.28), residues: 843 helix: 0.78 (0.22), residues: 576 sheet: None (None), residues: 0 loop : 1.19 (0.36), residues: 267 =============================================================================== Job complete usr+sys time: 2115.97 seconds wall clock time: 38 minutes 28.09 seconds (2308.09 seconds total)