Starting phenix.real_space_refine on Mon Sep 23 21:35:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrd_33414/09_2024/7xrd_33414.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrd_33414/09_2024/7xrd_33414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrd_33414/09_2024/7xrd_33414.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrd_33414/09_2024/7xrd_33414.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrd_33414/09_2024/7xrd_33414.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrd_33414/09_2024/7xrd_33414.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 24 5.16 5 C 3420 2.51 5 N 964 2.21 5 O 1036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 5460 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1332 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 5, 'TRANS': 158} Chain: "B" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1332 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 5, 'TRANS': 158} Chain: "C" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1332 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 5, 'TRANS': 158} Chain: "D" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1332 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 5, 'TRANS': 158} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.16, per 1000 atoms: 0.76 Number of scatterers: 5460 At special positions: 0 Unit cell: (91.3, 104.5, 86.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 24 16.00 P 12 15.00 Mg 4 11.99 O 1036 8.00 N 964 7.00 C 3420 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 580.4 milliseconds 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1216 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 5 sheets defined 43.8% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 67 through 78 Proline residue: A 72 - end of helix removed outlier: 3.862A pdb=" N TYR A 78 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 108 Processing helix chain 'A' and resid 110 through 115 removed outlier: 3.934A pdb=" N ARG A 113 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASP A 114 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 161 through 172 Processing helix chain 'B' and resid 25 through 35 Processing helix chain 'B' and resid 67 through 78 Proline residue: B 72 - end of helix removed outlier: 4.049A pdb=" N TYR B 78 " --> pdb=" O ARG B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 95 through 108 Processing helix chain 'B' and resid 110 through 115 removed outlier: 3.858A pdb=" N ARG B 113 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASP B 114 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 140 Processing helix chain 'B' and resid 141 through 144 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'C' and resid 25 through 35 Processing helix chain 'C' and resid 67 through 78 removed outlier: 3.542A pdb=" N ARG C 71 " --> pdb=" O ASP C 68 " (cutoff:3.500A) Proline residue: C 72 - end of helix removed outlier: 4.060A pdb=" N TYR C 78 " --> pdb=" O ARG C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 95 through 108 Processing helix chain 'C' and resid 110 through 115 removed outlier: 3.856A pdb=" N ARG C 113 " --> pdb=" O ARG C 110 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP C 114 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 Processing helix chain 'C' and resid 140 through 144 Processing helix chain 'C' and resid 161 through 172 Processing helix chain 'D' and resid 25 through 36 Processing helix chain 'D' and resid 67 through 78 Proline residue: D 72 - end of helix removed outlier: 3.881A pdb=" N TYR D 78 " --> pdb=" O ARG D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 108 Processing helix chain 'D' and resid 110 through 115 removed outlier: 3.863A pdb=" N ARG D 113 " --> pdb=" O ARG D 110 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP D 114 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 Processing helix chain 'D' and resid 140 through 144 Processing helix chain 'D' and resid 161 through 172 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 53 removed outlier: 6.801A pdb=" N LYS A 12 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASN A 60 " --> pdb=" O LYS A 12 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N MET A 14 " --> pdb=" O ASN A 60 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N TRP A 62 " --> pdb=" O MET A 14 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE A 16 " --> pdb=" O TRP A 62 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL A 64 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N MET A 18 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N GLY A 83 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG A 15 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE A 85 " --> pdb=" O ARG A 15 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 17 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL A 87 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 19 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ASP A 89 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 117 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N GLN A 152 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE A 119 " --> pdb=" O GLN A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 4.574A pdb=" N SER A 38 " --> pdb=" O THR C 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 53 removed outlier: 6.826A pdb=" N LYS B 12 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ASN B 60 " --> pdb=" O LYS B 12 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N MET B 14 " --> pdb=" O ASN B 60 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N TRP B 62 " --> pdb=" O MET B 14 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE B 16 " --> pdb=" O TRP B 62 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL B 64 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N MET B 18 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N GLY B 83 " --> pdb=" O GLU B 13 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG B 15 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE B 85 " --> pdb=" O ARG B 15 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 17 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL B 87 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU B 19 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N ASP B 89 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 47 through 53 removed outlier: 6.791A pdb=" N LYS C 12 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASN C 60 " --> pdb=" O LYS C 12 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N MET C 14 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N TRP C 62 " --> pdb=" O MET C 14 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE C 16 " --> pdb=" O TRP C 62 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL C 64 " --> pdb=" O ILE C 16 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N MET C 18 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N GLY C 83 " --> pdb=" O GLU C 13 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG C 15 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE C 85 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU C 17 " --> pdb=" O ILE C 85 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL C 87 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU C 19 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N ASP C 89 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 47 through 53 removed outlier: 6.757A pdb=" N LYS D 12 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ASN D 60 " --> pdb=" O LYS D 12 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N MET D 14 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N TRP D 62 " --> pdb=" O MET D 14 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE D 16 " --> pdb=" O TRP D 62 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL D 64 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N MET D 18 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N GLY D 83 " --> pdb=" O GLU D 13 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG D 15 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE D 85 " --> pdb=" O ARG D 15 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU D 17 " --> pdb=" O ILE D 85 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL D 87 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU D 19 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ASP D 89 " --> pdb=" O LEU D 19 " (cutoff:3.500A) 214 hydrogen bonds defined for protein. 552 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: 1.32 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1771 1.34 - 1.46: 1205 1.46 - 1.58: 2532 1.58 - 1.69: 20 1.69 - 1.81: 40 Bond restraints: 5568 Sorted by residual: bond pdb=" N LYS B 55 " pdb=" CA LYS B 55 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.86e-01 bond pdb=" C ARG A 71 " pdb=" N PRO A 72 " ideal model delta sigma weight residual 1.335 1.341 -0.006 1.19e-02 7.06e+03 2.62e-01 bond pdb=" CA GLY A 20 " pdb=" C GLY A 20 " ideal model delta sigma weight residual 1.509 1.515 -0.005 1.04e-02 9.25e+03 2.61e-01 bond pdb=" O3A GTP D 202 " pdb=" PB GTP D 202 " ideal model delta sigma weight residual 1.610 1.620 -0.010 2.00e-02 2.50e+03 2.48e-01 bond pdb=" C ILE B 42 " pdb=" N PRO B 43 " ideal model delta sigma weight residual 1.334 1.345 -0.012 2.34e-02 1.83e+03 2.45e-01 ... (remaining 5563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 7371 1.42 - 2.84: 149 2.84 - 4.26: 25 4.26 - 5.69: 13 5.69 - 7.11: 6 Bond angle restraints: 7564 Sorted by residual: angle pdb=" O3A GTP D 202 " pdb=" PB GTP D 202 " pdb=" O3B GTP D 202 " ideal model delta sigma weight residual 102.60 109.71 -7.11 3.00e+00 1.11e-01 5.61e+00 angle pdb=" C1' GTP B 202 " pdb=" C2' GTP B 202 " pdb=" C3' GTP B 202 " ideal model delta sigma weight residual 111.00 104.06 6.94 3.00e+00 1.11e-01 5.36e+00 angle pdb=" C1' GTP C 202 " pdb=" C2' GTP C 202 " pdb=" C3' GTP C 202 " ideal model delta sigma weight residual 111.00 104.11 6.89 3.00e+00 1.11e-01 5.28e+00 angle pdb=" C1' GTP D 202 " pdb=" C2' GTP D 202 " pdb=" C3' GTP D 202 " ideal model delta sigma weight residual 111.00 104.18 6.82 3.00e+00 1.11e-01 5.17e+00 angle pdb=" C1' GTP A 202 " pdb=" C2' GTP A 202 " pdb=" C3' GTP A 202 " ideal model delta sigma weight residual 111.00 104.24 6.76 3.00e+00 1.11e-01 5.07e+00 ... (remaining 7559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 3220 24.18 - 48.37: 65 48.37 - 72.55: 13 72.55 - 96.74: 6 96.74 - 120.92: 12 Dihedral angle restraints: 3316 sinusoidal: 1420 harmonic: 1896 Sorted by residual: dihedral pdb=" C8 GTP C 202 " pdb=" C1' GTP C 202 " pdb=" N9 GTP C 202 " pdb=" O4' GTP C 202 " ideal model delta sinusoidal sigma weight residual 104.59 -16.33 120.92 1 2.00e+01 2.50e-03 3.63e+01 dihedral pdb=" C8 GTP A 202 " pdb=" C1' GTP A 202 " pdb=" N9 GTP A 202 " pdb=" O4' GTP A 202 " ideal model delta sinusoidal sigma weight residual 104.59 -15.29 119.88 1 2.00e+01 2.50e-03 3.60e+01 dihedral pdb=" C8 GTP B 202 " pdb=" C1' GTP B 202 " pdb=" N9 GTP B 202 " pdb=" O4' GTP B 202 " ideal model delta sinusoidal sigma weight residual 104.59 -14.75 119.34 1 2.00e+01 2.50e-03 3.58e+01 ... (remaining 3313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 522 0.031 - 0.062: 185 0.062 - 0.093: 53 0.093 - 0.124: 62 0.124 - 0.155: 10 Chirality restraints: 832 Sorted by residual: chirality pdb=" CA ILE C 42 " pdb=" N ILE C 42 " pdb=" C ILE C 42 " pdb=" CB ILE C 42 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA ILE D 42 " pdb=" N ILE D 42 " pdb=" C ILE D 42 " pdb=" CB ILE D 42 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CA ILE A 42 " pdb=" N ILE A 42 " pdb=" C ILE A 42 " pdb=" CB ILE A 42 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 829 not shown) Planarity restraints: 940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 131 " -0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO C 132 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 132 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 132 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 131 " -0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO D 132 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 132 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 132 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 71 " -0.019 5.00e-02 4.00e+02 2.86e-02 1.30e+00 pdb=" N PRO B 72 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 72 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 72 " -0.016 5.00e-02 4.00e+02 ... (remaining 937 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 30 2.59 - 3.17: 4313 3.17 - 3.74: 7869 3.74 - 4.32: 11731 4.32 - 4.90: 18789 Nonbonded interactions: 42732 Sorted by model distance: nonbonded pdb=" OD2 ASP D 63 " pdb="MG MG D 201 " model vdw 2.012 2.170 nonbonded pdb=" OG1 THR A 27 " pdb="MG MG A 201 " model vdw 2.017 2.170 nonbonded pdb=" OG1 THR D 27 " pdb="MG MG D 201 " model vdw 2.024 2.170 nonbonded pdb=" OD2 ASP A 63 " pdb="MG MG A 201 " model vdw 2.041 2.170 nonbonded pdb=" OD1 ASP B 22 " pdb="MG MG B 201 " model vdw 2.074 2.170 ... (remaining 42727 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' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.300 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.510 Find NCS groups from input model: 0.200 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: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 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 : 0.002 0.013 5568 Z= 0.114 Angle : 0.575 7.107 7564 Z= 0.298 Chirality : 0.045 0.155 832 Planarity : 0.003 0.031 940 Dihedral : 14.120 120.919 2100 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.52 % Allowed : 0.69 % Favored : 98.78 % 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: -0.70 (0.32), residues: 648 helix: -1.41 (0.31), residues: 216 sheet: 0.16 (0.38), residues: 164 loop : 0.24 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 168 HIS 0.002 0.001 HIS D 76 PHE 0.005 0.001 PHE D 120 TYR 0.010 0.001 TYR A 77 ARG 0.002 0.000 ARG C 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 213 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 THR cc_start: 0.7924 (m) cc_final: 0.7711 (m) REVERT: B 130 MET cc_start: 0.7631 (mtm) cc_final: 0.7138 (mtm) REVERT: C 169 LEU cc_start: 0.8897 (mt) cc_final: 0.8614 (tt) REVERT: D 125 ASP cc_start: 0.8467 (p0) cc_final: 0.8013 (m-30) REVERT: D 131 LYS cc_start: 0.7896 (mppt) cc_final: 0.7643 (mmmt) outliers start: 3 outliers final: 0 residues processed: 216 average time/residue: 0.2942 time to fit residues: 74.0771 Evaluate side-chains 183 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN C 136 GLN C 148 ASN C 172 ASN D 104 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5568 Z= 0.254 Angle : 0.698 7.276 7564 Z= 0.344 Chirality : 0.050 0.171 832 Planarity : 0.005 0.040 940 Dihedral : 15.617 115.835 784 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.91 % Allowed : 11.28 % Favored : 86.81 % 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: -0.45 (0.32), residues: 648 helix: -0.38 (0.34), residues: 240 sheet: 0.09 (0.36), residues: 172 loop : -0.22 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 149 HIS 0.003 0.001 HIS D 76 PHE 0.016 0.002 PHE B 59 TYR 0.015 0.002 TYR B 163 ARG 0.008 0.001 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 186 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 28 THR cc_start: 0.8033 (m) cc_final: 0.7791 (m) REVERT: A 32 LYS cc_start: 0.9063 (tptt) cc_final: 0.8728 (tptt) REVERT: A 37 GLN cc_start: 0.8294 (mm-40) cc_final: 0.8030 (mp10) REVERT: A 71 ARG cc_start: 0.6773 (mmt-90) cc_final: 0.5261 (mmt-90) REVERT: B 73 LEU cc_start: 0.7884 (tp) cc_final: 0.7669 (tp) REVERT: B 123 LYS cc_start: 0.8619 (mttt) cc_final: 0.8271 (mttt) REVERT: B 130 MET cc_start: 0.7766 (mtm) cc_final: 0.6863 (mtm) REVERT: C 73 LEU cc_start: 0.8026 (tp) cc_final: 0.7713 (tp) REVERT: C 89 ASP cc_start: 0.8665 (t0) cc_final: 0.8440 (t0) REVERT: C 101 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7464 (mt0) REVERT: C 123 LYS cc_start: 0.9043 (mttt) cc_final: 0.8700 (mttt) REVERT: C 133 HIS cc_start: 0.6671 (p-80) cc_final: 0.6450 (p-80) REVERT: D 32 LYS cc_start: 0.9068 (tppt) cc_final: 0.8050 (tppt) REVERT: D 125 ASP cc_start: 0.8366 (p0) cc_final: 0.7900 (m-30) outliers start: 11 outliers final: 6 residues processed: 191 average time/residue: 0.2646 time to fit residues: 59.9706 Evaluate side-chains 193 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 187 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 70 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN B 136 GLN C 56 ASN C 172 ASN D 152 GLN D 172 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5568 Z= 0.310 Angle : 0.687 8.458 7564 Z= 0.340 Chirality : 0.051 0.162 832 Planarity : 0.004 0.033 940 Dihedral : 15.555 124.097 784 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.34 % Allowed : 12.33 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.32), residues: 648 helix: -0.26 (0.34), residues: 240 sheet: -0.02 (0.36), residues: 172 loop : -0.52 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 149 HIS 0.003 0.001 HIS A 104 PHE 0.016 0.002 PHE B 59 TYR 0.019 0.002 TYR A 150 ARG 0.006 0.001 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.9048 (tptt) cc_final: 0.8745 (tptt) REVERT: A 37 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8154 (mp10) REVERT: B 15 ARG cc_start: 0.7441 (mtp85) cc_final: 0.7061 (mtp85) REVERT: B 73 LEU cc_start: 0.8046 (tp) cc_final: 0.7816 (tp) REVERT: B 125 ASP cc_start: 0.8983 (p0) cc_final: 0.8752 (p0) REVERT: B 130 MET cc_start: 0.7817 (mtm) cc_final: 0.7453 (mtm) REVERT: C 73 LEU cc_start: 0.8143 (tp) cc_final: 0.7832 (tp) REVERT: C 133 HIS cc_start: 0.6784 (p-80) cc_final: 0.6501 (p-80) REVERT: D 32 LYS cc_start: 0.9133 (tppt) cc_final: 0.8854 (tppt) REVERT: D 54 TYR cc_start: 0.7788 (t80) cc_final: 0.6925 (t80) REVERT: D 70 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.9041 (mp) REVERT: D 125 ASP cc_start: 0.8506 (p0) cc_final: 0.7833 (m-30) outliers start: 25 outliers final: 12 residues processed: 190 average time/residue: 0.2655 time to fit residues: 59.5381 Evaluate side-chains 187 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 174 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 170 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 58 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5568 Z= 0.172 Angle : 0.613 6.532 7564 Z= 0.298 Chirality : 0.048 0.172 832 Planarity : 0.004 0.034 940 Dihedral : 14.374 118.487 784 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.65 % Allowed : 13.89 % Favored : 82.47 % 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: -0.16 (0.32), residues: 648 helix: 0.14 (0.35), residues: 236 sheet: 0.27 (0.36), residues: 172 loop : -0.43 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 168 HIS 0.003 0.001 HIS C 104 PHE 0.012 0.001 PHE B 59 TYR 0.012 0.001 TYR A 54 ARG 0.006 0.000 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.9023 (tptt) cc_final: 0.8695 (tptt) REVERT: A 125 ASP cc_start: 0.8653 (p0) cc_final: 0.7975 (m-30) REVERT: B 15 ARG cc_start: 0.7476 (mtp85) cc_final: 0.7113 (mtp85) REVERT: B 73 LEU cc_start: 0.8019 (tp) cc_final: 0.7762 (tp) REVERT: B 123 LYS cc_start: 0.8438 (mttt) cc_final: 0.8139 (mttp) REVERT: B 125 ASP cc_start: 0.8796 (p0) cc_final: 0.8593 (p0) REVERT: C 73 LEU cc_start: 0.8049 (tp) cc_final: 0.7741 (tp) REVERT: C 95 ARG cc_start: 0.7301 (ptp-170) cc_final: 0.7028 (ttm170) REVERT: C 122 ASN cc_start: 0.8900 (t0) cc_final: 0.8669 (t0) REVERT: C 133 HIS cc_start: 0.6792 (p-80) cc_final: 0.6490 (p-80) REVERT: C 174 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6933 (pttt) REVERT: D 32 LYS cc_start: 0.9131 (tppt) cc_final: 0.8866 (tppt) REVERT: D 125 ASP cc_start: 0.8483 (p0) cc_final: 0.7863 (m-30) REVERT: D 138 LYS cc_start: 0.8297 (mmmm) cc_final: 0.8061 (mtpp) outliers start: 21 outliers final: 11 residues processed: 172 average time/residue: 0.2729 time to fit residues: 55.3489 Evaluate side-chains 168 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 156 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 174 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 0.0000 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5568 Z= 0.209 Angle : 0.625 6.431 7564 Z= 0.305 Chirality : 0.049 0.175 832 Planarity : 0.004 0.036 940 Dihedral : 14.072 114.863 784 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.34 % Allowed : 15.10 % Favored : 80.56 % 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: -0.12 (0.32), residues: 648 helix: 0.31 (0.36), residues: 236 sheet: 0.29 (0.37), residues: 172 loop : -0.58 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 168 HIS 0.003 0.001 HIS C 104 PHE 0.012 0.002 PHE B 59 TYR 0.012 0.001 TYR A 150 ARG 0.006 0.000 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 158 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASP cc_start: 0.8679 (p0) cc_final: 0.8051 (m-30) REVERT: B 15 ARG cc_start: 0.7511 (mtp85) cc_final: 0.7203 (mtp85) REVERT: B 73 LEU cc_start: 0.8114 (tp) cc_final: 0.7836 (tp) REVERT: C 73 LEU cc_start: 0.8035 (tp) cc_final: 0.7707 (tp) REVERT: C 141 LEU cc_start: 0.8455 (mt) cc_final: 0.8243 (mt) REVERT: C 174 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.6781 (pttt) REVERT: D 32 LYS cc_start: 0.9139 (tppt) cc_final: 0.8873 (tppt) REVERT: D 125 ASP cc_start: 0.8455 (p0) cc_final: 0.7867 (m-30) REVERT: D 138 LYS cc_start: 0.8277 (mmmm) cc_final: 0.8025 (mtpp) outliers start: 25 outliers final: 16 residues processed: 173 average time/residue: 0.2649 time to fit residues: 54.2603 Evaluate side-chains 174 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 157 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain D residue 120 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5568 Z= 0.171 Angle : 0.616 6.605 7564 Z= 0.297 Chirality : 0.049 0.188 832 Planarity : 0.004 0.038 940 Dihedral : 13.565 111.589 784 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.99 % Allowed : 16.49 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.33), residues: 648 helix: 0.44 (0.36), residues: 236 sheet: 0.44 (0.38), residues: 172 loop : -0.68 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 168 HIS 0.002 0.001 HIS C 104 PHE 0.011 0.001 PHE B 59 TYR 0.020 0.001 TYR D 54 ARG 0.004 0.000 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.7356 (m110) cc_final: 0.6953 (m110) REVERT: A 125 ASP cc_start: 0.8662 (p0) cc_final: 0.8027 (m-30) REVERT: B 15 ARG cc_start: 0.7447 (mtp85) cc_final: 0.7105 (mtp85) REVERT: B 73 LEU cc_start: 0.8047 (tp) cc_final: 0.7778 (tp) REVERT: C 73 LEU cc_start: 0.8015 (tp) cc_final: 0.7687 (tp) REVERT: C 133 HIS cc_start: 0.6756 (p-80) cc_final: 0.6531 (p-80) REVERT: C 141 LEU cc_start: 0.8469 (mt) cc_final: 0.8250 (mt) REVERT: C 174 LYS cc_start: 0.7228 (OUTLIER) cc_final: 0.6811 (pttt) REVERT: D 32 LYS cc_start: 0.9133 (tppt) cc_final: 0.8888 (tppt) REVERT: D 125 ASP cc_start: 0.8391 (p0) cc_final: 0.7770 (m-30) outliers start: 23 outliers final: 14 residues processed: 167 average time/residue: 0.2700 time to fit residues: 53.0664 Evaluate side-chains 167 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 154 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 61 optimal weight: 0.0670 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 overall best weight: 2.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN C 56 ASN C 124 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5568 Z= 0.263 Angle : 0.656 6.716 7564 Z= 0.320 Chirality : 0.050 0.188 832 Planarity : 0.004 0.039 940 Dihedral : 13.884 113.289 784 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.34 % Allowed : 16.84 % Favored : 78.82 % 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: -0.21 (0.33), residues: 648 helix: 0.24 (0.36), residues: 236 sheet: 0.39 (0.38), residues: 172 loop : -0.78 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 168 HIS 0.003 0.001 HIS B 104 PHE 0.011 0.002 PHE D 120 TYR 0.013 0.001 TYR A 150 ARG 0.003 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.7461 (m110) cc_final: 0.7009 (m110) REVERT: A 125 ASP cc_start: 0.8610 (p0) cc_final: 0.7979 (m-30) REVERT: B 15 ARG cc_start: 0.7448 (mtp85) cc_final: 0.7092 (mtp85) REVERT: B 73 LEU cc_start: 0.8125 (tp) cc_final: 0.7866 (tp) REVERT: B 101 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7755 (mt0) REVERT: C 73 LEU cc_start: 0.8092 (tp) cc_final: 0.7770 (tp) REVERT: C 89 ASP cc_start: 0.8481 (t0) cc_final: 0.8092 (t0) REVERT: C 123 LYS cc_start: 0.8549 (mttt) cc_final: 0.8148 (mttp) REVERT: C 141 LEU cc_start: 0.8464 (mt) cc_final: 0.8253 (mt) REVERT: C 174 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.6924 (pttt) REVERT: D 32 LYS cc_start: 0.9101 (tppt) cc_final: 0.8814 (tppt) REVERT: D 54 TYR cc_start: 0.7574 (t80) cc_final: 0.6975 (t80) REVERT: D 125 ASP cc_start: 0.8387 (p0) cc_final: 0.7712 (m-30) outliers start: 25 outliers final: 13 residues processed: 177 average time/residue: 0.2656 time to fit residues: 55.5526 Evaluate side-chains 176 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 154 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 0.0670 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN C 56 ASN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.5557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5568 Z= 0.311 Angle : 0.695 7.135 7564 Z= 0.342 Chirality : 0.052 0.188 832 Planarity : 0.004 0.044 940 Dihedral : 14.084 115.211 784 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.82 % Allowed : 18.23 % Favored : 77.95 % 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: -0.33 (0.33), residues: 648 helix: 0.14 (0.35), residues: 236 sheet: 0.32 (0.39), residues: 172 loop : -0.84 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 149 HIS 0.004 0.001 HIS B 104 PHE 0.014 0.002 PHE D 120 TYR 0.013 0.002 TYR A 150 ARG 0.004 0.000 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 165 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.7303 (m110) cc_final: 0.6765 (m110) REVERT: A 112 MET cc_start: 0.7317 (mmm) cc_final: 0.6994 (mtp) REVERT: A 125 ASP cc_start: 0.8636 (p0) cc_final: 0.7987 (m-30) REVERT: B 73 LEU cc_start: 0.8181 (tp) cc_final: 0.7910 (tp) REVERT: C 73 LEU cc_start: 0.8153 (tp) cc_final: 0.7822 (tp) REVERT: C 141 LEU cc_start: 0.8455 (mt) cc_final: 0.8244 (mt) REVERT: C 174 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.6915 (pttt) REVERT: D 32 LYS cc_start: 0.9068 (tppt) cc_final: 0.8800 (tppt) REVERT: D 125 ASP cc_start: 0.8398 (p0) cc_final: 0.7672 (m-30) outliers start: 22 outliers final: 13 residues processed: 173 average time/residue: 0.2690 time to fit residues: 54.8341 Evaluate side-chains 175 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 161 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 154 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 0.0010 chunk 57 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.5630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5568 Z= 0.174 Angle : 0.646 7.547 7564 Z= 0.312 Chirality : 0.050 0.196 832 Planarity : 0.004 0.040 940 Dihedral : 13.308 110.226 784 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.12 % Allowed : 18.75 % Favored : 78.12 % 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: -0.11 (0.34), residues: 648 helix: 0.35 (0.36), residues: 236 sheet: 0.31 (0.39), residues: 184 loop : -0.68 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 62 HIS 0.002 0.001 HIS C 104 PHE 0.009 0.001 PHE B 59 TYR 0.017 0.001 TYR D 54 ARG 0.003 0.000 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.7391 (m110) cc_final: 0.6926 (m110) REVERT: A 125 ASP cc_start: 0.8621 (p0) cc_final: 0.8037 (m-30) REVERT: B 73 LEU cc_start: 0.8085 (tp) cc_final: 0.7826 (tp) REVERT: B 101 GLN cc_start: 0.8240 (mm-40) cc_final: 0.7815 (mt0) REVERT: B 102 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7013 (mm-30) REVERT: C 73 LEU cc_start: 0.8056 (tp) cc_final: 0.7741 (tp) REVERT: C 113 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7622 (ptm160) REVERT: C 122 ASN cc_start: 0.9000 (t0) cc_final: 0.8753 (t0) REVERT: C 141 LEU cc_start: 0.8491 (mt) cc_final: 0.8270 (mt) REVERT: C 174 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.6922 (pttt) REVERT: D 32 LYS cc_start: 0.9022 (tppt) cc_final: 0.8793 (tppt) REVERT: D 108 ASN cc_start: 0.7438 (m-40) cc_final: 0.7209 (m110) REVERT: D 125 ASP cc_start: 0.8470 (p0) cc_final: 0.7774 (m-30) REVERT: D 131 LYS cc_start: 0.8242 (mppt) cc_final: 0.7801 (mmmt) outliers start: 18 outliers final: 10 residues processed: 168 average time/residue: 0.2896 time to fit residues: 57.0805 Evaluate side-chains 167 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 155 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 154 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 39 optimal weight: 0.0980 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 54 optimal weight: 0.3980 chunk 15 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN C 124 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5568 Z= 0.160 Angle : 0.672 7.780 7564 Z= 0.320 Chirality : 0.049 0.202 832 Planarity : 0.004 0.042 940 Dihedral : 12.724 104.615 784 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.08 % Allowed : 20.31 % Favored : 77.60 % 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: 0.03 (0.34), residues: 648 helix: 0.50 (0.35), residues: 236 sheet: 0.36 (0.39), residues: 184 loop : -0.62 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 62 HIS 0.002 0.001 HIS C 104 PHE 0.009 0.001 PHE B 59 TYR 0.020 0.001 TYR D 54 ARG 0.008 0.000 ARG B 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 156 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8882 (tptt) cc_final: 0.8616 (tptp) REVERT: A 108 ASN cc_start: 0.7396 (m110) cc_final: 0.6925 (m110) REVERT: A 125 ASP cc_start: 0.8541 (p0) cc_final: 0.7948 (m-30) REVERT: B 73 LEU cc_start: 0.8050 (tp) cc_final: 0.7763 (tp) REVERT: B 101 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7864 (mt0) REVERT: B 102 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7032 (mm-30) REVERT: C 73 LEU cc_start: 0.8068 (tp) cc_final: 0.7765 (tp) REVERT: C 141 LEU cc_start: 0.8516 (mt) cc_final: 0.8301 (mt) REVERT: C 174 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.6923 (pttt) REVERT: D 32 LYS cc_start: 0.9021 (tppt) cc_final: 0.8753 (tppt) REVERT: D 108 ASN cc_start: 0.7397 (m-40) cc_final: 0.7100 (m110) REVERT: D 125 ASP cc_start: 0.8419 (p0) cc_final: 0.7744 (m-30) REVERT: D 131 LYS cc_start: 0.8248 (mppt) cc_final: 0.7741 (mmmt) outliers start: 12 outliers final: 8 residues processed: 161 average time/residue: 0.2748 time to fit residues: 52.1184 Evaluate side-chains 157 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 148 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 154 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 50 optimal weight: 0.0270 chunk 21 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 0.2980 chunk 58 optimal weight: 0.1980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.127596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.104462 restraints weight = 7086.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.107777 restraints weight = 4704.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.110312 restraints weight = 3495.907| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.5920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5568 Z= 0.153 Angle : 0.665 7.890 7564 Z= 0.315 Chirality : 0.049 0.207 832 Planarity : 0.004 0.043 940 Dihedral : 12.238 99.942 784 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.56 % Allowed : 21.53 % Favored : 76.91 % 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: 0.41 (0.34), residues: 648 helix: 1.01 (0.36), residues: 216 sheet: 0.20 (0.37), residues: 196 loop : -0.18 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 62 HIS 0.004 0.001 HIS B 104 PHE 0.009 0.001 PHE D 59 TYR 0.026 0.001 TYR D 54 ARG 0.004 0.000 ARG D 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1857.85 seconds wall clock time: 33 minutes 21.01 seconds (2001.01 seconds total)