Starting phenix.real_space_refine on Sun Dec 29 02:37:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b7v_15903/12_2024/8b7v_15903.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b7v_15903/12_2024/8b7v_15903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b7v_15903/12_2024/8b7v_15903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b7v_15903/12_2024/8b7v_15903.map" model { file = "/net/cci-nas-00/data/ceres_data/8b7v_15903/12_2024/8b7v_15903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b7v_15903/12_2024/8b7v_15903.cif" } resolution = 3.0 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 6330 2.51 5 N 1713 2.21 5 O 1965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10050 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3350 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 412} Chain: "B" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3350 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 412} Chain: "C" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3350 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 412} Time building chain proxies: 5.95, per 1000 atoms: 0.59 Number of scatterers: 10050 At special positions: 0 Unit cell: (97.11, 96.28, 76.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1965 8.00 N 1713 7.00 C 6330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 38 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 38 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 38 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.1 seconds 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2238 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 12 sheets defined 4.0% alpha, 57.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 113 through 116 Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 397 through 401 Processing helix chain 'B' and resid 113 through 116 Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 238 through 240 No H-bonds generated for 'chain 'B' and resid 238 through 240' Processing helix chain 'B' and resid 397 through 401 Processing helix chain 'C' and resid 113 through 116 Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.566A pdb=" N ASP C 162 " --> pdb=" O ASN C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 240 No H-bonds generated for 'chain 'C' and resid 238 through 240' Processing helix chain 'C' and resid 397 through 401 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 14 removed outlier: 4.015A pdb=" N LEU A 46 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 62 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE A 58 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS A 52 " --> pdb=" O LYS A 56 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ALA A 65 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N PHE A 81 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU A 139 " --> pdb=" O ASN A 131 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 142 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY A 150 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASN A 165 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A 168 " --> pdb=" O ASN A 197 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 178 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LEU A 187 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLU A 180 " --> pdb=" O GLY A 185 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N GLY A 185 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP A 213 " --> pdb=" O THR A 236 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 112 removed outlier: 3.516A pdb=" N TRP A 120 " --> pdb=" O HIS A 110 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL A 112 " --> pdb=" O TYR A 118 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR A 118 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 254 Processing sheet with id=AA4, first strand: chain 'A' and resid 376 through 378 Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 14 removed outlier: 3.968A pdb=" N LEU B 46 " --> pdb=" O THR B 62 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 62 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE B 58 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS B 52 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LYS B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA B 65 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N PHE B 81 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 11.618A pdb=" N GLY B 124 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 10.464A pdb=" N SER B 147 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLY B 126 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ARG B 145 " --> pdb=" O GLY B 126 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLY B 128 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ALA B 143 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU B 130 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 141 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 142 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY B 150 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASN B 165 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B 168 " --> pdb=" O ASN B 197 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU B 187 " --> pdb=" O GLN B 178 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP B 213 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N MET B 320 " --> pdb=" O TRP B 316 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 112 removed outlier: 6.898A pdb=" N HIS B 110 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 252 through 254 Processing sheet with id=AA8, first strand: chain 'B' and resid 376 through 378 Processing sheet with id=AA9, first strand: chain 'C' and resid 203 through 204 removed outlier: 4.081A pdb=" N ALA C 142 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY C 150 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASN C 165 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA C 168 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LEU C 187 " --> pdb=" O GLN C 178 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLU C 180 " --> pdb=" O GLY C 185 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N GLY C 185 " --> pdb=" O GLU C 180 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TRP C 213 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP C 284 " --> pdb=" O MET C 280 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N MET C 320 " --> pdb=" O TRP C 316 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU C 46 " --> pdb=" O THR C 62 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR C 62 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE C 58 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS C 52 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS C 56 " --> pdb=" O LYS C 52 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER C 57 " --> pdb=" O GLY C 88 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLY C 88 " --> pdb=" O SER C 57 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TYR C 59 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL C 86 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASP C 61 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 84 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ASN C 63 " --> pdb=" O ARG C 82 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU C 139 " --> pdb=" O ASN C 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 112 removed outlier: 6.659A pdb=" N VAL C 112 " --> pdb=" O TYR C 118 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N TYR C 118 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 252 through 254 Processing sheet with id=AB3, first strand: chain 'C' and resid 376 through 379 removed outlier: 4.020A pdb=" N LYS C 392 " --> pdb=" O ASP C 379 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1551 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: 3.56 Time building geometry restraints manager: 3.07 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: 2204 1.34 - 1.46: 3960 1.46 - 1.58: 4087 1.58 - 1.71: 0 1.71 - 1.83: 78 Bond restraints: 10329 Sorted by residual: bond pdb=" CD ARG B 335 " pdb=" NE ARG B 335 " ideal model delta sigma weight residual 1.458 1.510 -0.052 1.40e-02 5.10e+03 1.39e+01 bond pdb=" CD ARG C 335 " pdb=" NE ARG C 335 " ideal model delta sigma weight residual 1.458 1.510 -0.052 1.40e-02 5.10e+03 1.36e+01 bond pdb=" CD ARG A 335 " pdb=" NE ARG A 335 " ideal model delta sigma weight residual 1.458 1.509 -0.051 1.40e-02 5.10e+03 1.31e+01 bond pdb=" CE1 HIS B 275 " pdb=" NE2 HIS B 275 " ideal model delta sigma weight residual 1.321 1.357 -0.036 1.00e-02 1.00e+04 1.30e+01 bond pdb=" CE1 HIS C 275 " pdb=" NE2 HIS C 275 " ideal model delta sigma weight residual 1.321 1.357 -0.036 1.00e-02 1.00e+04 1.27e+01 ... (remaining 10324 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 10932 2.09 - 4.18: 2642 4.18 - 6.28: 391 6.28 - 8.37: 43 8.37 - 10.46: 2 Bond angle restraints: 14010 Sorted by residual: angle pdb=" CA ARG C 360 " pdb=" C ARG C 360 " pdb=" N PRO C 361 " ideal model delta sigma weight residual 117.68 126.03 -8.35 7.10e-01 1.98e+00 1.38e+02 angle pdb=" CA THR B 317 " pdb=" C THR B 317 " pdb=" N PRO B 318 " ideal model delta sigma weight residual 117.96 125.95 -7.99 8.10e-01 1.52e+00 9.72e+01 angle pdb=" CA THR C 317 " pdb=" C THR C 317 " pdb=" N PRO C 318 " ideal model delta sigma weight residual 117.96 125.52 -7.56 8.10e-01 1.52e+00 8.71e+01 angle pdb=" CA ARG B 360 " pdb=" C ARG B 360 " pdb=" N PRO B 361 " ideal model delta sigma weight residual 117.95 125.05 -7.10 7.70e-01 1.69e+00 8.50e+01 angle pdb=" CA ASP A 211 " pdb=" CB ASP A 211 " pdb=" CG ASP A 211 " ideal model delta sigma weight residual 112.60 119.94 -7.34 1.00e+00 1.00e+00 5.39e+01 ... (remaining 14005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.77: 5385 18.77 - 37.54: 313 37.54 - 56.32: 60 56.32 - 75.09: 58 75.09 - 93.86: 22 Dihedral angle restraints: 5838 sinusoidal: 2274 harmonic: 3564 Sorted by residual: dihedral pdb=" N GLN B 70 " pdb=" C GLN B 70 " pdb=" CA GLN B 70 " pdb=" CB GLN B 70 " ideal model delta harmonic sigma weight residual 122.80 137.61 -14.81 0 2.50e+00 1.60e-01 3.51e+01 dihedral pdb=" CA TYR B 32 " pdb=" C TYR B 32 " pdb=" N ARG B 33 " pdb=" CA ARG B 33 " ideal model delta harmonic sigma weight residual -180.00 -150.66 -29.34 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" C GLN B 70 " pdb=" N GLN B 70 " pdb=" CA GLN B 70 " pdb=" CB GLN B 70 " ideal model delta harmonic sigma weight residual -122.60 -137.11 14.51 0 2.50e+00 1.60e-01 3.37e+01 ... (remaining 5835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1021 0.116 - 0.232: 284 0.232 - 0.348: 53 0.348 - 0.464: 7 0.464 - 0.580: 3 Chirality restraints: 1368 Sorted by residual: chirality pdb=" CA GLN B 70 " pdb=" N GLN B 70 " pdb=" C GLN B 70 " pdb=" CB GLN B 70 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.40e+00 chirality pdb=" CA GLN A 70 " pdb=" N GLN A 70 " pdb=" C GLN A 70 " pdb=" CB GLN A 70 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.63e+00 chirality pdb=" CA GLN C 70 " pdb=" N GLN C 70 " pdb=" C GLN C 70 " pdb=" CB GLN C 70 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.84e+00 ... (remaining 1365 not shown) Planarity restraints: 1854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 118 " -0.202 2.00e-02 2.50e+03 1.21e-01 2.91e+02 pdb=" CG TYR C 118 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR C 118 " 0.078 2.00e-02 2.50e+03 pdb=" CD2 TYR C 118 " 0.087 2.00e-02 2.50e+03 pdb=" CE1 TYR C 118 " 0.075 2.00e-02 2.50e+03 pdb=" CE2 TYR C 118 " 0.089 2.00e-02 2.50e+03 pdb=" CZ TYR C 118 " 0.043 2.00e-02 2.50e+03 pdb=" OH TYR C 118 " -0.211 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 118 " -0.164 2.00e-02 2.50e+03 9.65e-02 1.86e+02 pdb=" CG TYR A 118 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR A 118 " 0.073 2.00e-02 2.50e+03 pdb=" CD2 TYR A 118 " 0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR A 118 " 0.066 2.00e-02 2.50e+03 pdb=" CE2 TYR A 118 " 0.060 2.00e-02 2.50e+03 pdb=" CZ TYR A 118 " 0.036 2.00e-02 2.50e+03 pdb=" OH TYR A 118 " -0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 32 " 0.125 2.00e-02 2.50e+03 7.29e-02 1.06e+02 pdb=" CG TYR A 32 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 32 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR A 32 " -0.051 2.00e-02 2.50e+03 pdb=" CE1 TYR A 32 " -0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR A 32 " -0.049 2.00e-02 2.50e+03 pdb=" CZ TYR A 32 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR A 32 " 0.124 2.00e-02 2.50e+03 ... (remaining 1851 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 3752 2.91 - 3.41: 8290 3.41 - 3.90: 17791 3.90 - 4.40: 19949 4.40 - 4.90: 35305 Nonbonded interactions: 85087 Sorted by model distance: nonbonded pdb=" N THR B 317 " pdb=" O THR B 317 " model vdw 2.409 2.496 nonbonded pdb=" N THR C 317 " pdb=" O THR C 317 " model vdw 2.425 2.496 nonbonded pdb=" N ARG C 360 " pdb=" O ARG C 360 " model vdw 2.449 2.496 nonbonded pdb=" N THR A 317 " pdb=" O THR A 317 " model vdw 2.465 2.496 nonbonded pdb=" N ARG B 360 " pdb=" O ARG B 360 " model vdw 2.488 2.496 ... (remaining 85082 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=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: 0.170 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: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.360 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 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 : 0.015 0.052 10329 Z= 0.958 Angle : 1.804 10.461 14010 Z= 1.245 Chirality : 0.114 0.580 1368 Planarity : 0.019 0.276 1854 Dihedral : 15.921 93.858 3591 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 0.05 Ramachandran Plot: Outliers : 0.64 % Allowed : 2.63 % Favored : 96.74 % Rotamer: Outliers : 1.76 % Allowed : 5.29 % Favored : 92.94 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 12.50 % 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: -0.16 (0.21), residues: 1257 helix: -4.93 (0.16), residues: 18 sheet: 1.57 (0.19), residues: 612 loop : -1.85 (0.20), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.015 TRP A 51 HIS 0.012 0.003 HIS A 4 PHE 0.076 0.011 PHE C 254 TYR 0.211 0.022 TYR C 118 ARG 0.042 0.005 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 1.229 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 2 residues processed: 146 average time/residue: 1.6958 time to fit residues: 262.6776 Evaluate side-chains 76 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain B residue 420 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 HIS A 70 GLN A 349 GLN B 4 HIS B 70 GLN B 90 ASN C 4 HIS C 70 GLN C 159 ASN C 165 ASN C 341 ASN C 386 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10329 Z= 0.261 Angle : 0.634 5.616 14010 Z= 0.362 Chirality : 0.046 0.148 1368 Planarity : 0.004 0.064 1854 Dihedral : 6.309 61.099 1381 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.27 % Favored : 98.57 % Rotamer: Outliers : 2.65 % Allowed : 8.53 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.24 (0.21), residues: 1257 helix: -4.98 (0.13), residues: 18 sheet: 1.24 (0.19), residues: 600 loop : -1.50 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 120 HIS 0.004 0.001 HIS A 113 PHE 0.009 0.001 PHE B 58 TYR 0.012 0.001 TYR A 343 ARG 0.008 0.001 ARG C 360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 179 MET cc_start: 0.6280 (OUTLIER) cc_final: 0.5713 (mtm) outliers start: 27 outliers final: 0 residues processed: 89 average time/residue: 1.5216 time to fit residues: 144.6657 Evaluate side-chains 57 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 114 optimal weight: 30.0000 chunk 123 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 ASN C 416 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10329 Z= 0.281 Angle : 0.598 8.344 14010 Z= 0.335 Chirality : 0.045 0.148 1368 Planarity : 0.004 0.064 1854 Dihedral : 5.596 23.937 1377 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.75 % Favored : 98.09 % Rotamer: Outliers : 1.67 % Allowed : 9.80 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.39 (0.21), residues: 1257 helix: -5.05 (0.12), residues: 18 sheet: 0.97 (0.20), residues: 606 loop : -1.43 (0.20), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 120 HIS 0.004 0.001 HIS A 113 PHE 0.011 0.001 PHE C 23 TYR 0.016 0.001 TYR A 343 ARG 0.004 0.000 ARG C 360 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 1.167 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 0 residues processed: 80 average time/residue: 1.5735 time to fit residues: 134.0293 Evaluate side-chains 61 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 59 optimal weight: 30.0000 chunk 12 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN B 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10329 Z= 0.333 Angle : 0.590 7.348 14010 Z= 0.331 Chirality : 0.044 0.145 1368 Planarity : 0.004 0.062 1854 Dihedral : 5.414 19.543 1377 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.99 % Favored : 97.85 % Rotamer: Outliers : 1.08 % Allowed : 10.49 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.46 (0.21), residues: 1257 helix: -5.07 (0.11), residues: 18 sheet: 0.86 (0.20), residues: 609 loop : -1.41 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 420 HIS 0.003 0.001 HIS B 113 PHE 0.007 0.001 PHE B 23 TYR 0.015 0.001 TYR A 343 ARG 0.006 0.001 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 1.232 Fit side-chains outliers start: 11 outliers final: 1 residues processed: 72 average time/residue: 1.6513 time to fit residues: 126.7808 Evaluate side-chains 57 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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: 0.7166 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10329 Z= 0.309 Angle : 0.576 6.727 14010 Z= 0.323 Chirality : 0.044 0.140 1368 Planarity : 0.004 0.063 1854 Dihedral : 5.359 22.708 1377 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.91 % Favored : 97.93 % Rotamer: Outliers : 1.27 % Allowed : 11.18 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.50 (0.22), residues: 1257 helix: -5.06 (0.11), residues: 18 sheet: 0.84 (0.20), residues: 597 loop : -1.40 (0.21), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 420 HIS 0.003 0.001 HIS B 113 PHE 0.006 0.001 PHE A 254 TYR 0.014 0.001 TYR A 343 ARG 0.005 0.000 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 1.166 Fit side-chains outliers start: 13 outliers final: 3 residues processed: 70 average time/residue: 1.6024 time to fit residues: 119.7826 Evaluate side-chains 59 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 417 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 30.0000 chunk 109 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 121 optimal weight: 30.0000 chunk 101 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 117 optimal weight: 9.9990 overall best weight: 8.7994 ------------------------------------------------------------------------------- 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: 0.7180 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 10329 Z= 0.356 Angle : 0.596 6.533 14010 Z= 0.332 Chirality : 0.044 0.140 1368 Planarity : 0.004 0.060 1854 Dihedral : 5.329 23.450 1377 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.15 % Favored : 97.69 % Rotamer: Outliers : 0.98 % Allowed : 12.06 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.59 (0.22), residues: 1257 helix: -5.07 (0.11), residues: 18 sheet: 0.77 (0.20), residues: 600 loop : -1.46 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 420 HIS 0.003 0.001 HIS B 113 PHE 0.007 0.001 PHE A 254 TYR 0.015 0.001 TYR A 343 ARG 0.004 0.001 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 1.223 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 66 average time/residue: 1.6235 time to fit residues: 115.1359 Evaluate side-chains 57 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 417 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 76 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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: 0.7176 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10329 Z= 0.321 Angle : 0.583 6.129 14010 Z= 0.326 Chirality : 0.043 0.137 1368 Planarity : 0.004 0.059 1854 Dihedral : 5.269 27.426 1377 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.07 % Favored : 97.77 % Rotamer: Outliers : 1.08 % Allowed : 12.35 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.62 (0.22), residues: 1257 helix: -5.07 (0.11), residues: 18 sheet: 0.72 (0.20), residues: 600 loop : -1.45 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 94 HIS 0.003 0.001 HIS B 113 PHE 0.007 0.001 PHE B 23 TYR 0.014 0.001 TYR A 343 ARG 0.004 0.000 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 1.164 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 66 average time/residue: 1.5176 time to fit residues: 107.4767 Evaluate side-chains 59 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 417 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 23 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 30.0000 chunk 60 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 110 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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: 0.7160 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10329 Z= 0.269 Angle : 0.581 7.534 14010 Z= 0.322 Chirality : 0.043 0.139 1368 Planarity : 0.004 0.059 1854 Dihedral : 5.214 25.456 1377 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.15 % Favored : 97.69 % Rotamer: Outliers : 0.49 % Allowed : 13.24 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.69 (0.22), residues: 1257 helix: -5.06 (0.11), residues: 18 sheet: 0.56 (0.21), residues: 582 loop : -1.32 (0.21), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 94 HIS 0.002 0.001 HIS C 113 PHE 0.006 0.001 PHE B 23 TYR 0.013 0.001 TYR B 343 ARG 0.004 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 1.113 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 62 average time/residue: 1.4625 time to fit residues: 97.5477 Evaluate side-chains 57 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 147 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 68 optimal weight: 30.0000 chunk 49 optimal weight: 5.9990 chunk 88 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 119 optimal weight: 0.4980 overall best weight: 5.8988 ------------------------------------------------------------------------------- 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: 0.7157 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10329 Z= 0.259 Angle : 0.588 9.199 14010 Z= 0.323 Chirality : 0.043 0.139 1368 Planarity : 0.004 0.058 1854 Dihedral : 5.145 24.425 1377 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.23 % Favored : 97.61 % Rotamer: Outliers : 0.78 % Allowed : 13.14 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 (0.22), residues: 1257 helix: -5.06 (0.11), residues: 18 sheet: 0.64 (0.20), residues: 588 loop : -1.28 (0.21), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 94 HIS 0.002 0.001 HIS C 113 PHE 0.006 0.001 PHE B 23 TYR 0.013 0.001 TYR B 343 ARG 0.004 0.000 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 1.133 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 63 average time/residue: 1.5493 time to fit residues: 104.4876 Evaluate side-chains 56 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 147 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 99 optimal weight: 40.0000 chunk 10 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 106 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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: 0.7152 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10329 Z= 0.251 Angle : 0.579 8.708 14010 Z= 0.319 Chirality : 0.043 0.139 1368 Planarity : 0.004 0.059 1854 Dihedral : 5.106 25.674 1377 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.23 % Favored : 97.61 % Rotamer: Outliers : 0.39 % Allowed : 13.43 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.63 (0.22), residues: 1257 helix: -5.06 (0.11), residues: 18 sheet: 0.55 (0.20), residues: 603 loop : -1.28 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 94 HIS 0.002 0.001 HIS A 113 PHE 0.006 0.001 PHE B 23 TYR 0.013 0.001 TYR B 343 ARG 0.004 0.000 ARG B 360 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 1.235 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 57 average time/residue: 1.4889 time to fit residues: 91.3671 Evaluate side-chains 56 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 147 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 100 optimal weight: 30.0000 chunk 41 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN B 349 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.065363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.052854 restraints weight = 20812.449| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 3.05 r_work: 0.2500 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10329 Z= 0.346 Angle : 0.617 8.693 14010 Z= 0.339 Chirality : 0.044 0.137 1368 Planarity : 0.004 0.063 1854 Dihedral : 5.203 26.040 1377 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.39 % Favored : 97.45 % Rotamer: Outliers : 0.39 % Allowed : 13.73 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.64 (0.22), residues: 1257 helix: -5.06 (0.11), residues: 18 sheet: 0.57 (0.20), residues: 600 loop : -1.29 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 94 HIS 0.003 0.001 HIS C 113 PHE 0.008 0.001 PHE C 117 TYR 0.015 0.001 TYR A 343 ARG 0.005 0.001 ARG C 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2600.16 seconds wall clock time: 48 minutes 13.79 seconds (2893.79 seconds total)