Starting phenix.real_space_refine on Mon Sep 23 21:44:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qb9_13882/09_2024/7qb9_13882.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qb9_13882/09_2024/7qb9_13882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qb9_13882/09_2024/7qb9_13882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qb9_13882/09_2024/7qb9_13882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qb9_13882/09_2024/7qb9_13882.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qb9_13882/09_2024/7qb9_13882.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.119 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 21 5.16 5 C 3732 2.51 5 N 732 2.21 5 O 934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5419 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2295 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 290} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2298 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 290} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 413 Unusual residues: {'NAG': 2, 'Y01': 11} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 413 Unusual residues: {'NAG': 2, 'Y01': 11} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.14, per 1000 atoms: 0.76 Number of scatterers: 5419 At special positions: 0 Unit cell: (81.2736, 83.8134, 100.745, 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 21 16.00 O 934 8.00 N 732 7.00 C 3732 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 - 3.00 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 25 " " NAG A 502 " - " ASN A 32 " " NAG B 501 " - " ASN B 25 " " NAG B 502 " - " ASN B 32 " Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 602.5 milliseconds 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1136 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 2 sheets defined 75.3% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 9 through 14 removed outlier: 3.506A pdb=" N PHE A 12 " --> pdb=" O SER A 9 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP A 14 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 73 removed outlier: 3.638A pdb=" N SER A 47 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET A 54 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A 55 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 103 removed outlier: 3.856A pdb=" N LEU A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 103 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 114 Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.600A pdb=" N ILE A 120 " --> pdb=" O PRO A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 154 removed outlier: 3.806A pdb=" N THR A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN A 132 " --> pdb=" O TYR A 128 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 153 " --> pdb=" O GLN A 149 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 195 removed outlier: 4.070A pdb=" N THR A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 236 removed outlier: 3.705A pdb=" N PHE A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 Processing helix chain 'A' and resid 256 through 266 removed outlier: 3.745A pdb=" N PHE A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 272 Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.653A pdb=" N THR A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 297 Proline residue: A 290 - end of helix removed outlier: 3.714A pdb=" N MET A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 14 removed outlier: 3.505A pdb=" N PHE B 12 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP B 14 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 73 removed outlier: 3.637A pdb=" N SER B 47 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE B 53 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET B 54 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE B 55 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 103 removed outlier: 3.857A pdb=" N LEU B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE B 89 " --> pdb=" O GLN B 85 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.601A pdb=" N ILE B 120 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 154 removed outlier: 3.806A pdb=" N THR B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN B 132 " --> pdb=" O TYR B 128 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL B 136 " --> pdb=" O ASN B 132 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE B 153 " --> pdb=" O GLN B 149 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 195 removed outlier: 4.069A pdb=" N THR B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU B 173 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 236 removed outlier: 3.668A pdb=" N PHE B 235 " --> pdb=" O ARG B 231 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'B' and resid 256 through 266 removed outlier: 3.746A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 272 Processing helix chain 'B' and resid 273 through 278 removed outlier: 3.653A pdb=" N THR B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 297 Proline residue: B 290 - end of helix removed outlier: 3.714A pdb=" N MET B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 28 removed outlier: 6.507A pdb=" N SER A 28 " --> pdb=" O ASN A 32 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASN A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 28 removed outlier: 6.507A pdb=" N SER B 28 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASN B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 749 1.31 - 1.44: 1357 1.44 - 1.56: 3413 1.56 - 1.68: 22 1.68 - 1.81: 38 Bond restraints: 5579 Sorted by residual: bond pdb=" C7 NAG B 501 " pdb=" N2 NAG B 501 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C7 NAG A 501 " pdb=" N2 NAG A 501 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C7 NAG A 502 " pdb=" N2 NAG A 502 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C7 NAG B 502 " pdb=" N2 NAG B 502 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C1 NAG B 502 " pdb=" O5 NAG B 502 " ideal model delta sigma weight residual 1.406 1.510 -0.104 2.00e-02 2.50e+03 2.69e+01 ... (remaining 5574 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 7140 1.80 - 3.61: 472 3.61 - 5.41: 85 5.41 - 7.21: 16 7.21 - 9.02: 4 Bond angle restraints: 7717 Sorted by residual: angle pdb=" N PHE B 204 " pdb=" CA PHE B 204 " pdb=" C PHE B 204 " ideal model delta sigma weight residual 111.54 106.03 5.51 1.36e+00 5.41e-01 1.64e+01 angle pdb=" N PHE A 204 " pdb=" CA PHE A 204 " pdb=" C PHE A 204 " ideal model delta sigma weight residual 111.54 106.24 5.30 1.36e+00 5.41e-01 1.52e+01 angle pdb=" N PHE B 235 " pdb=" CA PHE B 235 " pdb=" C PHE B 235 " ideal model delta sigma weight residual 111.28 107.10 4.18 1.09e+00 8.42e-01 1.47e+01 angle pdb=" N TYR B 106 " pdb=" CA TYR B 106 " pdb=" C TYR B 106 " ideal model delta sigma weight residual 113.23 108.60 4.63 1.24e+00 6.50e-01 1.39e+01 angle pdb=" N PHE A 235 " pdb=" CA PHE A 235 " pdb=" C PHE A 235 " ideal model delta sigma weight residual 111.28 107.23 4.05 1.09e+00 8.42e-01 1.38e+01 ... (remaining 7712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 3918 15.26 - 30.52: 345 30.52 - 45.78: 83 45.78 - 61.03: 51 61.03 - 76.29: 4 Dihedral angle restraints: 4401 sinusoidal: 2643 harmonic: 1758 Sorted by residual: dihedral pdb=" CA ILE A 263 " pdb=" C ILE A 263 " pdb=" N LEU A 264 " pdb=" CA LEU A 264 " ideal model delta harmonic sigma weight residual 180.00 160.44 19.56 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ILE B 263 " pdb=" C ILE B 263 " pdb=" N LEU B 264 " pdb=" CA LEU B 264 " ideal model delta harmonic sigma weight residual 180.00 160.48 19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" N ASN A 25 " pdb=" C ASN A 25 " pdb=" CA ASN A 25 " pdb=" CB ASN A 25 " ideal model delta harmonic sigma weight residual 122.80 114.48 8.32 0 2.50e+00 1.60e-01 1.11e+01 ... (remaining 4398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 883 0.079 - 0.157: 98 0.157 - 0.236: 12 0.236 - 0.314: 5 0.314 - 0.393: 2 Chirality restraints: 1000 Sorted by residual: chirality pdb=" CBC Y01 A 513 " pdb=" CAR Y01 A 513 " pdb=" CAV Y01 A 513 " pdb=" OAW Y01 A 513 " both_signs ideal model delta sigma weight residual False -2.54 -2.15 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CBC Y01 A 509 " pdb=" CAR Y01 A 509 " pdb=" CAV Y01 A 509 " pdb=" OAW Y01 A 509 " both_signs ideal model delta sigma weight residual False -2.54 -2.19 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CA ASN A 25 " pdb=" N ASN A 25 " pdb=" C ASN A 25 " pdb=" CB ASN A 25 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 997 not shown) Planarity restraints: 820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 269 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.85e+01 pdb=" N PRO A 270 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO A 270 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 270 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 269 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.85e+01 pdb=" N PRO B 270 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 247 " -0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C LEU B 247 " 0.068 2.00e-02 2.50e+03 pdb=" O LEU B 247 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU B 248 " -0.023 2.00e-02 2.50e+03 ... (remaining 817 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1313 2.81 - 3.33: 4887 3.33 - 3.86: 7972 3.86 - 4.38: 9176 4.38 - 4.90: 16024 Nonbonded interactions: 39372 Sorted by model distance: nonbonded pdb=" O ILE B 175 " pdb=" OG1 THR B 179 " model vdw 2.291 3.040 nonbonded pdb=" O ILE A 175 " pdb=" OG1 THR A 179 " model vdw 2.291 3.040 nonbonded pdb=" O ALA B 61 " pdb=" OG1 THR B 65 " model vdw 2.317 3.040 nonbonded pdb=" O ALA A 61 " pdb=" OG1 THR A 65 " model vdw 2.317 3.040 nonbonded pdb=" O ASN A 46 " pdb=" OG1 THR A 50 " model vdw 2.340 3.040 ... (remaining 39367 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' and (resid 5 through 249 or (resid 250 and (name N or name CA or name \ C or name O or name CB )) or resid 251 through 303 or resid 501 through 513)) } 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.790 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 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 0.128 5579 Z= 0.473 Angle : 1.013 9.016 7717 Z= 0.545 Chirality : 0.056 0.393 1000 Planarity : 0.010 0.108 816 Dihedral : 12.615 76.292 3265 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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: -2.92 (0.29), residues: 594 helix: -1.69 (0.22), residues: 416 sheet: None (None), residues: 0 loop : -2.11 (0.37), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 70 HIS 0.004 0.002 HIS B 94 PHE 0.042 0.003 PHE A 262 TYR 0.025 0.002 TYR B 266 ARG 0.003 0.000 ARG A 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.658 Fit side-chains REVERT: A 218 MET cc_start: 0.8242 (tpt) cc_final: 0.7568 (tpt) REVERT: B 180 MET cc_start: 0.7601 (tpt) cc_final: 0.7273 (tpp) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1738 time to fit residues: 11.3975 Evaluate side-chains 42 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5579 Z= 0.176 Angle : 0.545 5.937 7717 Z= 0.274 Chirality : 0.039 0.281 1000 Planarity : 0.005 0.065 816 Dihedral : 9.668 59.434 2284 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.97 % Allowed : 6.41 % Favored : 92.62 % 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: -0.52 (0.33), residues: 594 helix: 0.32 (0.25), residues: 416 sheet: None (None), residues: 0 loop : -1.83 (0.39), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 70 HIS 0.004 0.001 HIS B 94 PHE 0.024 0.002 PHE B 244 TYR 0.019 0.001 TYR B 266 ARG 0.003 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.557 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 50 average time/residue: 0.1462 time to fit residues: 10.2871 Evaluate side-chains 42 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain B residue 190 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 43 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5579 Z= 0.168 Angle : 0.499 5.051 7717 Z= 0.246 Chirality : 0.037 0.209 1000 Planarity : 0.004 0.052 816 Dihedral : 9.393 59.708 2284 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.75 % Allowed : 7.57 % Favored : 90.68 % 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: 0.73 (0.35), residues: 594 helix: 1.30 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -1.48 (0.42), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 70 HIS 0.004 0.001 HIS B 94 PHE 0.014 0.002 PHE B 244 TYR 0.018 0.001 TYR A 266 ARG 0.003 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 228 LEU cc_start: 0.7694 (tt) cc_final: 0.7485 (mm) outliers start: 9 outliers final: 6 residues processed: 55 average time/residue: 0.1430 time to fit residues: 11.0376 Evaluate side-chains 48 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 244 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.3980 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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: 0.7800 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5579 Z= 0.186 Angle : 0.515 5.072 7717 Z= 0.249 Chirality : 0.039 0.181 1000 Planarity : 0.004 0.048 816 Dihedral : 9.256 57.738 2284 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.33 % Allowed : 9.13 % Favored : 88.54 % 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: 1.12 (0.35), residues: 594 helix: 1.59 (0.27), residues: 416 sheet: None (None), residues: 0 loop : -1.31 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 70 HIS 0.004 0.001 HIS B 94 PHE 0.016 0.001 PHE A 55 TYR 0.014 0.001 TYR A 266 ARG 0.003 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 PHE cc_start: 0.7036 (OUTLIER) cc_final: 0.6148 (m-80) REVERT: B 228 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7452 (tt) outliers start: 12 outliers final: 7 residues processed: 57 average time/residue: 0.1458 time to fit residues: 11.7354 Evaluate side-chains 57 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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: 0.7895 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5579 Z= 0.289 Angle : 0.616 5.771 7717 Z= 0.291 Chirality : 0.042 0.177 1000 Planarity : 0.004 0.047 816 Dihedral : 9.640 59.584 2284 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.72 % Allowed : 10.29 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.35), residues: 594 helix: 1.54 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.43 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 295 HIS 0.005 0.001 HIS A 94 PHE 0.020 0.002 PHE B 55 TYR 0.017 0.001 TYR B 266 ARG 0.005 0.001 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 45 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: B 151 LYS cc_start: 0.7563 (ttmt) cc_final: 0.7228 (ttmm) REVERT: B 228 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7332 (tt) outliers start: 14 outliers final: 12 residues processed: 52 average time/residue: 0.1534 time to fit residues: 11.0062 Evaluate side-chains 57 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 44 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 244 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 54 optimal weight: 0.0770 chunk 6 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.0270 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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: 0.7758 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5579 Z= 0.124 Angle : 0.474 4.952 7717 Z= 0.230 Chirality : 0.037 0.209 1000 Planarity : 0.003 0.044 816 Dihedral : 9.069 59.986 2284 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.52 % Allowed : 10.10 % Favored : 87.38 % 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: 1.74 (0.36), residues: 594 helix: 2.12 (0.27), residues: 416 sheet: None (None), residues: 0 loop : -1.26 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 70 HIS 0.003 0.001 HIS B 94 PHE 0.013 0.001 PHE A 171 TYR 0.013 0.001 TYR A 266 ARG 0.001 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 49 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 PHE cc_start: 0.7074 (OUTLIER) cc_final: 0.6329 (m-80) REVERT: B 228 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7216 (tt) REVERT: B 244 PHE cc_start: 0.7006 (OUTLIER) cc_final: 0.6273 (m-80) outliers start: 13 outliers final: 6 residues processed: 60 average time/residue: 0.1357 time to fit residues: 11.3996 Evaluate side-chains 55 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 244 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.0670 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- 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: 0.7813 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5579 Z= 0.187 Angle : 0.509 5.054 7717 Z= 0.244 Chirality : 0.039 0.215 1000 Planarity : 0.003 0.044 816 Dihedral : 9.112 58.525 2284 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.33 % Allowed : 11.46 % Favored : 86.21 % 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: 1.82 (0.36), residues: 594 helix: 2.25 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.26 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 70 HIS 0.004 0.001 HIS B 94 PHE 0.014 0.001 PHE B 55 TYR 0.015 0.001 TYR A 266 ARG 0.002 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 48 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 PHE cc_start: 0.7105 (OUTLIER) cc_final: 0.6318 (m-80) REVERT: B 228 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7273 (tt) REVERT: B 244 PHE cc_start: 0.7047 (OUTLIER) cc_final: 0.6239 (m-80) outliers start: 12 outliers final: 8 residues processed: 56 average time/residue: 0.1393 time to fit residues: 10.8887 Evaluate side-chains 59 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 244 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.2980 chunk 48 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7750 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5579 Z= 0.130 Angle : 0.459 4.963 7717 Z= 0.222 Chirality : 0.037 0.187 1000 Planarity : 0.003 0.044 816 Dihedral : 8.830 58.466 2284 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.33 % Allowed : 11.65 % Favored : 86.02 % 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: 2.20 (0.36), residues: 594 helix: 2.53 (0.27), residues: 408 sheet: None (None), residues: 0 loop : -1.09 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 70 HIS 0.003 0.001 HIS A 94 PHE 0.013 0.001 PHE B 244 TYR 0.013 0.001 TYR A 266 ARG 0.001 0.000 ARG A 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 PHE cc_start: 0.7063 (OUTLIER) cc_final: 0.6357 (m-80) REVERT: B 228 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7303 (tt) REVERT: B 244 PHE cc_start: 0.7039 (OUTLIER) cc_final: 0.6321 (m-80) outliers start: 12 outliers final: 9 residues processed: 56 average time/residue: 0.1411 time to fit residues: 11.2003 Evaluate side-chains 57 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 244 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 0.0050 chunk 46 optimal weight: 0.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN B 51 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5579 Z= 0.172 Angle : 0.494 5.040 7717 Z= 0.236 Chirality : 0.038 0.206 1000 Planarity : 0.003 0.044 816 Dihedral : 8.915 58.503 2284 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.33 % Allowed : 12.23 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.36), residues: 594 helix: 2.42 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -1.15 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 70 HIS 0.004 0.001 HIS B 94 PHE 0.013 0.001 PHE B 55 TYR 0.015 0.001 TYR A 266 ARG 0.002 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 PHE cc_start: 0.7127 (OUTLIER) cc_final: 0.6374 (m-80) REVERT: B 228 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7292 (tt) REVERT: B 244 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.6296 (m-80) outliers start: 12 outliers final: 9 residues processed: 57 average time/residue: 0.1662 time to fit residues: 13.3935 Evaluate side-chains 61 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 244 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5579 Z= 0.145 Angle : 0.472 5.004 7717 Z= 0.227 Chirality : 0.037 0.187 1000 Planarity : 0.003 0.044 816 Dihedral : 8.803 57.327 2284 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.33 % Allowed : 12.23 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.36), residues: 594 helix: 2.52 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -1.04 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 70 HIS 0.003 0.001 HIS B 94 PHE 0.012 0.001 PHE B 244 TYR 0.014 0.001 TYR A 266 ARG 0.001 0.000 ARG A 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 PHE cc_start: 0.7101 (OUTLIER) cc_final: 0.6391 (m-80) REVERT: B 228 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7246 (tt) REVERT: B 244 PHE cc_start: 0.7046 (OUTLIER) cc_final: 0.6301 (m-80) outliers start: 12 outliers final: 9 residues processed: 55 average time/residue: 0.1461 time to fit residues: 11.2428 Evaluate side-chains 57 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 244 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.175704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.117953 restraints weight = 5641.566| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.46 r_work: 0.3180 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5579 Z= 0.162 Angle : 0.486 5.041 7717 Z= 0.232 Chirality : 0.038 0.187 1000 Planarity : 0.003 0.044 816 Dihedral : 8.809 56.449 2284 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.33 % Allowed : 12.43 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.36), residues: 594 helix: 2.50 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -1.06 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 70 HIS 0.003 0.001 HIS B 94 PHE 0.013 0.001 PHE B 55 TYR 0.015 0.001 TYR A 266 ARG 0.002 0.000 ARG B 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1254.70 seconds wall clock time: 23 minutes 1.00 seconds (1381.00 seconds total)