Starting phenix.real_space_refine on Sun Sep 13 05:12:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mqf_23945/09_2026/7mqf_23945.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mqf_23945/09_2026/7mqf_23945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7mqf_23945/09_2026/7mqf_23945.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mqf_23945/09_2026/7mqf_23945.cif" model { file = "/net/cci-nas-00/data/ceres_data/7mqf_23945/09_2026/7mqf_23945.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mqf_23945/09_2026/7mqf_23945.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mqf_23945/09_2026/7mqf_23945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mqf_23945/09_2026/7mqf_23945.map" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11200 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 48 5.16 5 C 7800 2.51 5 N 2248 2.21 5 O 2176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12288 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1490 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 7, 'ARG:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNAv2': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Restraints were copied for chains: C, E, G, I, K, M, O, D, F, H, J, L, N, P Time building chain proxies: 1.62, per 1000 atoms: 0.13 Number of scatterers: 12288 At special positions: 0 Unit cell: (104.78, 104.78, 86.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 16 15.00 O 2176 8.00 N 2248 7.00 C 7800 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 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 423.0 milliseconds 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3056 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 46.3% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 80 through 93 removed outlier: 3.993A pdb=" N ASP A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 110 Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 145 through 155 removed outlier: 3.624A pdb=" N ASP A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 175 through 196 Proline residue: A 187 - end of helix Processing helix chain 'C' and resid 62 through 71 Processing helix chain 'C' and resid 80 through 93 removed outlier: 3.995A pdb=" N ASP C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 86 " --> pdb=" O ARG C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 110 Processing helix chain 'C' and resid 117 through 127 Processing helix chain 'C' and resid 145 through 155 removed outlier: 3.624A pdb=" N ASP C 155 " --> pdb=" O TYR C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 173 Processing helix chain 'C' and resid 175 through 196 Proline residue: C 187 - end of helix Processing helix chain 'E' and resid 62 through 71 Processing helix chain 'E' and resid 80 through 93 removed outlier: 3.994A pdb=" N ASP E 84 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA E 86 " --> pdb=" O ARG E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'E' and resid 117 through 127 Processing helix chain 'E' and resid 145 through 155 removed outlier: 3.623A pdb=" N ASP E 155 " --> pdb=" O TYR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 173 Processing helix chain 'E' and resid 175 through 196 Proline residue: E 187 - end of helix Processing helix chain 'G' and resid 62 through 71 Processing helix chain 'G' and resid 80 through 93 removed outlier: 3.994A pdb=" N ASP G 84 " --> pdb=" O PHE G 80 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA G 86 " --> pdb=" O ARG G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 110 Processing helix chain 'G' and resid 117 through 127 Processing helix chain 'G' and resid 145 through 155 removed outlier: 3.623A pdb=" N ASP G 155 " --> pdb=" O TYR G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 173 Processing helix chain 'G' and resid 175 through 196 Proline residue: G 187 - end of helix Processing helix chain 'I' and resid 62 through 71 Processing helix chain 'I' and resid 80 through 93 removed outlier: 3.994A pdb=" N ASP I 84 " --> pdb=" O PHE I 80 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA I 86 " --> pdb=" O ARG I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 110 Processing helix chain 'I' and resid 117 through 127 Processing helix chain 'I' and resid 145 through 155 removed outlier: 3.623A pdb=" N ASP I 155 " --> pdb=" O TYR I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 173 Processing helix chain 'I' and resid 175 through 196 Proline residue: I 187 - end of helix Processing helix chain 'K' and resid 62 through 71 Processing helix chain 'K' and resid 80 through 93 removed outlier: 3.994A pdb=" N ASP K 84 " --> pdb=" O PHE K 80 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA K 86 " --> pdb=" O ARG K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 110 Processing helix chain 'K' and resid 117 through 127 Processing helix chain 'K' and resid 145 through 155 removed outlier: 3.623A pdb=" N ASP K 155 " --> pdb=" O TYR K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 173 Processing helix chain 'K' and resid 175 through 196 Proline residue: K 187 - end of helix Processing helix chain 'M' and resid 62 through 71 Processing helix chain 'M' and resid 80 through 93 removed outlier: 3.994A pdb=" N ASP M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA M 86 " --> pdb=" O ARG M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 110 Processing helix chain 'M' and resid 117 through 127 Processing helix chain 'M' and resid 145 through 155 removed outlier: 3.623A pdb=" N ASP M 155 " --> pdb=" O TYR M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 173 Processing helix chain 'M' and resid 175 through 196 Proline residue: M 187 - end of helix Processing helix chain 'O' and resid 62 through 71 Processing helix chain 'O' and resid 80 through 93 removed outlier: 3.994A pdb=" N ASP O 84 " --> pdb=" O PHE O 80 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA O 86 " --> pdb=" O ARG O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 110 Processing helix chain 'O' and resid 117 through 127 Processing helix chain 'O' and resid 145 through 155 removed outlier: 3.623A pdb=" N ASP O 155 " --> pdb=" O TYR O 151 " (cutoff:3.500A) Processing helix chain 'O' and resid 158 through 173 Processing helix chain 'O' and resid 175 through 196 Proline residue: O 187 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.236A pdb=" N ARG A 5 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN A 54 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS A 7 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL A 22 " --> pdb=" O ILE A 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.236A pdb=" N ARG C 5 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN C 54 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS C 7 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL C 22 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.235A pdb=" N ARG E 5 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN E 54 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N HIS E 7 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL E 22 " --> pdb=" O ILE E 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 4 through 8 removed outlier: 6.236A pdb=" N ARG G 5 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN G 54 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS G 7 " --> pdb=" O GLN G 54 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL G 22 " --> pdb=" O ILE G 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 4 through 8 removed outlier: 6.236A pdb=" N ARG I 5 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN I 54 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS I 7 " --> pdb=" O GLN I 54 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL I 22 " --> pdb=" O ILE I 77 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 4 through 8 removed outlier: 6.236A pdb=" N ARG K 5 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN K 54 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS K 7 " --> pdb=" O GLN K 54 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL K 22 " --> pdb=" O ILE K 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 4 through 8 removed outlier: 6.236A pdb=" N ARG M 5 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN M 54 " --> pdb=" O ARG M 5 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N HIS M 7 " --> pdb=" O GLN M 54 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL M 22 " --> pdb=" O ILE M 77 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 4 through 8 removed outlier: 6.236A pdb=" N ARG O 5 " --> pdb=" O VAL O 52 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN O 54 " --> pdb=" O ARG O 5 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS O 7 " --> pdb=" O GLN O 54 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL O 22 " --> pdb=" O ILE O 77 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1704 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: 1.77 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4053 1.34 - 1.46: 1823 1.46 - 1.57: 6580 1.57 - 1.69: 24 1.69 - 1.81: 64 Bond restraints: 12544 Sorted by residual: bond pdb=" CG LYS A 103 " pdb=" CD LYS A 103 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.68e-01 bond pdb=" CG LYS M 103 " pdb=" CD LYS M 103 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.68e-01 bond pdb=" CG LYS I 103 " pdb=" CD LYS I 103 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.68e-01 bond pdb=" CG LYS K 103 " pdb=" CD LYS K 103 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.68e-01 bond pdb=" CG LYS O 103 " pdb=" CD LYS O 103 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.68e-01 ... (remaining 12539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 15481 1.13 - 2.25: 1399 2.25 - 3.38: 144 3.38 - 4.50: 85 4.50 - 5.63: 35 Bond angle restraints: 17144 Sorted by residual: angle pdb=" CB LYS E 103 " pdb=" CG LYS E 103 " pdb=" CD LYS E 103 " ideal model delta sigma weight residual 111.30 116.93 -5.63 2.30e+00 1.89e-01 5.98e+00 angle pdb=" CB LYS C 103 " pdb=" CG LYS C 103 " pdb=" CD LYS C 103 " ideal model delta sigma weight residual 111.30 116.92 -5.62 2.30e+00 1.89e-01 5.98e+00 angle pdb=" N ARG M 67 " pdb=" CA ARG M 67 " pdb=" CB ARG M 67 " ideal model delta sigma weight residual 110.12 113.71 -3.59 1.47e+00 4.63e-01 5.97e+00 angle pdb=" N ARG A 67 " pdb=" CA ARG A 67 " pdb=" CB ARG A 67 " ideal model delta sigma weight residual 110.12 113.71 -3.59 1.47e+00 4.63e-01 5.97e+00 angle pdb=" CB LYS O 103 " pdb=" CG LYS O 103 " pdb=" CD LYS O 103 " ideal model delta sigma weight residual 111.30 116.90 -5.60 2.30e+00 1.89e-01 5.93e+00 ... (remaining 17139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.04: 6824 15.04 - 30.08: 392 30.08 - 45.12: 88 45.12 - 60.16: 32 60.16 - 75.20: 16 Dihedral angle restraints: 7352 sinusoidal: 2672 harmonic: 4680 Sorted by residual: dihedral pdb=" CA PHE K 78 " pdb=" C PHE K 78 " pdb=" N HIS K 79 " pdb=" CA HIS K 79 " ideal model delta harmonic sigma weight residual 180.00 157.41 22.59 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA PHE A 78 " pdb=" C PHE A 78 " pdb=" N HIS A 79 " pdb=" CA HIS A 79 " ideal model delta harmonic sigma weight residual 180.00 157.42 22.58 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA PHE M 78 " pdb=" C PHE M 78 " pdb=" N HIS M 79 " pdb=" CA HIS M 79 " ideal model delta harmonic sigma weight residual 180.00 157.44 22.56 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 7349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1639 0.069 - 0.139: 421 0.139 - 0.208: 4 0.208 - 0.277: 8 0.277 - 0.346: 8 Chirality restraints: 2080 Sorted by residual: chirality pdb=" P G D 603 " pdb=" OP1 G D 603 " pdb=" OP2 G D 603 " pdb=" O5' G D 603 " both_signs ideal model delta sigma weight residual True 2.17 2.52 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" P G N 603 " pdb=" OP1 G N 603 " pdb=" OP2 G N 603 " pdb=" O5' G N 603 " both_signs ideal model delta sigma weight residual True 2.17 2.52 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" P G F 603 " pdb=" OP1 G F 603 " pdb=" OP2 G F 603 " pdb=" O5' G F 603 " both_signs ideal model delta sigma weight residual True 2.17 2.52 -0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 2077 not shown) Planarity restraints: 2120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE I 83 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" C PHE I 83 " 0.026 2.00e-02 2.50e+03 pdb=" O PHE I 83 " -0.010 2.00e-02 2.50e+03 pdb=" N ASP I 84 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE K 83 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.12e+00 pdb=" C PHE K 83 " -0.025 2.00e-02 2.50e+03 pdb=" O PHE K 83 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP K 84 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 83 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.10e+00 pdb=" C PHE C 83 " -0.025 2.00e-02 2.50e+03 pdb=" O PHE C 83 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP C 84 " 0.008 2.00e-02 2.50e+03 ... (remaining 2117 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 431 2.72 - 3.26: 11698 3.26 - 3.81: 19601 3.81 - 4.35: 26977 4.35 - 4.90: 44034 Nonbonded interactions: 102741 Sorted by model distance: nonbonded pdb=" NZ LYS G 107 " pdb=" O ALA O 204 " model vdw 2.175 3.120 nonbonded pdb=" O ALA G 204 " pdb=" NZ LYS O 107 " model vdw 2.175 3.120 nonbonded pdb=" NZ LYS E 107 " pdb=" O ALA I 204 " model vdw 2.175 3.120 nonbonded pdb=" NZ LYS A 107 " pdb=" O ALA M 204 " model vdw 2.175 3.120 nonbonded pdb=" O ALA E 204 " pdb=" NZ LYS I 107 " model vdw 2.176 3.120 ... (remaining 102736 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } 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: 1.640 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.570 Find NCS groups from input model: 0.130 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:8.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 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 : 0.006 0.030 12544 Z= 0.248 Angle : 0.731 5.625 17144 Z= 0.413 Chirality : 0.061 0.346 2080 Planarity : 0.004 0.025 2120 Dihedral : 11.488 75.197 4296 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.21), residues: 1576 helix: 0.74 (0.19), residues: 704 sheet: 0.56 (0.23), residues: 248 loop : 1.35 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 37 TYR 0.015 0.002 TYR M 17 PHE 0.016 0.002 PHE K 78 TRP 0.005 0.002 TRP E 139 HIS 0.006 0.002 HIS E 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.25 (12544) covalent geometry : angle 0.73122 / 0.41 (17144) hydrogen bonds : bond 0.11553 / 7.58 ( 568) hydrogen bonds : angle 7.42616 / 5.38 ( 1704) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.424 Fit side-chains REVERT: A 151 TYR cc_start: 0.6969 (t80) cc_final: 0.6165 (m-80) REVERT: C 151 TYR cc_start: 0.6919 (t80) cc_final: 0.6157 (m-80) REVERT: E 151 TYR cc_start: 0.6973 (t80) cc_final: 0.6159 (m-80) REVERT: G 151 TYR cc_start: 0.6973 (t80) cc_final: 0.6157 (m-80) REVERT: I 151 TYR cc_start: 0.6967 (t80) cc_final: 0.6162 (m-80) REVERT: K 151 TYR cc_start: 0.6965 (t80) cc_final: 0.6160 (m-80) REVERT: M 151 TYR cc_start: 0.6958 (t80) cc_final: 0.6149 (m-80) REVERT: O 151 TYR cc_start: 0.6968 (t80) cc_final: 0.6160 (m-80) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.5835 time to fit residues: 101.3843 Evaluate side-chains 129 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN C 13 ASN E 13 ASN G 13 ASN I 13 ASN K 13 ASN M 13 ASN O 13 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.110268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.094075 restraints weight = 13389.149| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 0.94 r_work: 0.2769 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9086 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 12544 Z= 0.150 Angle : 0.522 4.687 17144 Z= 0.280 Chirality : 0.047 0.140 2080 Planarity : 0.004 0.025 2120 Dihedral : 5.118 23.951 1896 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 0.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.21), residues: 1576 helix: 1.97 (0.20), residues: 704 sheet: 0.89 (0.24), residues: 248 loop : 0.94 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 169 TYR 0.011 0.002 TYR K 17 PHE 0.013 0.002 PHE C 78 TRP 0.003 0.001 TRP I 139 HIS 0.004 0.001 HIS E 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (12544) covalent geometry : angle 0.52211 / 0.28 (17144) hydrogen bonds : bond 0.04791 / 3.22 ( 568) hydrogen bonds : angle 5.73783 / 4.15 ( 1704) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.469 Fit side-chains REVERT: A 151 TYR cc_start: 0.7684 (t80) cc_final: 0.6806 (m-80) REVERT: C 151 TYR cc_start: 0.7659 (t80) cc_final: 0.6787 (m-80) REVERT: E 151 TYR cc_start: 0.7667 (t80) cc_final: 0.6802 (m-80) REVERT: G 151 TYR cc_start: 0.7671 (t80) cc_final: 0.6804 (m-80) REVERT: I 151 TYR cc_start: 0.7669 (t80) cc_final: 0.6793 (m-80) REVERT: K 151 TYR cc_start: 0.7673 (t80) cc_final: 0.6806 (m-80) REVERT: M 151 TYR cc_start: 0.7674 (t80) cc_final: 0.6796 (m-80) REVERT: O 151 TYR cc_start: 0.7664 (t80) cc_final: 0.6798 (m-80) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.5675 time to fit residues: 83.4970 Evaluate side-chains 128 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 71 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 73 optimal weight: 0.0270 chunk 81 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN C 13 ASN E 13 ASN G 13 ASN I 13 ASN K 13 ASN M 13 ASN O 13 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.111582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.095759 restraints weight = 13369.776| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 0.92 r_work: 0.2837 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 12544 Z= 0.105 Angle : 0.440 4.426 17144 Z= 0.240 Chirality : 0.044 0.131 2080 Planarity : 0.003 0.024 2120 Dihedral : 4.698 21.079 1896 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 0.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.21), residues: 1576 helix: 1.97 (0.20), residues: 704 sheet: 0.93 (0.23), residues: 248 loop : 0.70 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 5 TYR 0.008 0.001 TYR C 17 PHE 0.012 0.001 PHE C 78 TRP 0.001 0.001 TRP C 139 HIS 0.003 0.001 HIS E 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (12544) covalent geometry : angle 0.43986 / 0.24 (17144) hydrogen bonds : bond 0.04013 / 2.70 ( 568) hydrogen bonds : angle 5.38352 / 3.90 ( 1704) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.479 Fit side-chains REVERT: A 151 TYR cc_start: 0.7568 (t80) cc_final: 0.6732 (m-80) REVERT: C 151 TYR cc_start: 0.7535 (t80) cc_final: 0.6733 (m-80) REVERT: E 151 TYR cc_start: 0.7565 (t80) cc_final: 0.6735 (m-80) REVERT: G 151 TYR cc_start: 0.7577 (t80) cc_final: 0.6731 (m-80) REVERT: I 151 TYR cc_start: 0.7556 (t80) cc_final: 0.6722 (m-80) REVERT: K 151 TYR cc_start: 0.7563 (t80) cc_final: 0.6729 (m-80) REVERT: M 151 TYR cc_start: 0.7568 (t80) cc_final: 0.6732 (m-80) REVERT: O 151 TYR cc_start: 0.7573 (t80) cc_final: 0.6727 (m-80) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.5004 time to fit residues: 69.1824 Evaluate side-chains 121 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 3 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 9 optimal weight: 0.0770 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 overall best weight: 4.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN C 13 ASN E 13 ASN G 13 ASN I 13 ASN K 13 ASN M 13 ASN O 13 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.108250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.090708 restraints weight = 13407.282| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 1.05 r_work: 0.2718 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 12544 Z= 0.219 Angle : 0.572 5.449 17144 Z= 0.300 Chirality : 0.050 0.152 2080 Planarity : 0.004 0.030 2120 Dihedral : 5.207 21.155 1896 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 0.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.21), residues: 1576 helix: 1.54 (0.19), residues: 704 sheet: 1.03 (0.24), residues: 248 loop : 0.36 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 169 TYR 0.012 0.003 TYR I 17 PHE 0.012 0.002 PHE C 78 TRP 0.003 0.001 TRP C 139 HIS 0.005 0.002 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 (12544) covalent geometry : angle 0.57163 / 0.30 (17144) hydrogen bonds : bond 0.05380 / 3.62 ( 568) hydrogen bonds : angle 5.58056 / 4.04 ( 1704) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.485 Fit side-chains REVERT: A 151 TYR cc_start: 0.7792 (t80) cc_final: 0.6883 (m-80) REVERT: C 151 TYR cc_start: 0.7775 (t80) cc_final: 0.6885 (m-80) REVERT: E 151 TYR cc_start: 0.7778 (t80) cc_final: 0.6879 (m-80) REVERT: G 151 TYR cc_start: 0.7793 (t80) cc_final: 0.6890 (m-80) REVERT: I 151 TYR cc_start: 0.7777 (t80) cc_final: 0.6892 (m-80) REVERT: K 151 TYR cc_start: 0.7788 (t80) cc_final: 0.6887 (m-80) REVERT: M 151 TYR cc_start: 0.7785 (t80) cc_final: 0.6882 (m-80) REVERT: O 151 TYR cc_start: 0.7782 (t80) cc_final: 0.6879 (m-80) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.4776 time to fit residues: 68.0317 Evaluate side-chains 129 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 20 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 81 optimal weight: 0.0370 chunk 90 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 overall best weight: 2.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 GLN C 8 GLN E 8 GLN E 13 ASN G 8 GLN I 8 GLN K 8 GLN M 8 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.109779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.093590 restraints weight = 13430.035| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 0.93 r_work: 0.2762 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9100 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 12544 Z= 0.155 Angle : 0.496 4.430 17144 Z= 0.265 Chirality : 0.046 0.140 2080 Planarity : 0.004 0.029 2120 Dihedral : 4.959 20.737 1896 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.21), residues: 1576 helix: 1.54 (0.19), residues: 704 sheet: 0.96 (0.23), residues: 248 loop : 0.24 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 5 TYR 0.010 0.002 TYR E 17 PHE 0.012 0.002 PHE C 78 TRP 0.002 0.001 TRP E 139 HIS 0.004 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (12544) covalent geometry : angle 0.49611 / 0.26 (17144) hydrogen bonds : bond 0.04688 / 3.15 ( 568) hydrogen bonds : angle 5.42006 / 3.92 ( 1704) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.457 Fit side-chains REVERT: A 151 TYR cc_start: 0.7707 (t80) cc_final: 0.6868 (m-80) REVERT: C 151 TYR cc_start: 0.7694 (t80) cc_final: 0.6853 (m-80) REVERT: E 151 TYR cc_start: 0.7708 (t80) cc_final: 0.6868 (m-80) REVERT: G 151 TYR cc_start: 0.7714 (t80) cc_final: 0.6876 (m-80) REVERT: I 151 TYR cc_start: 0.7710 (t80) cc_final: 0.6866 (m-80) REVERT: K 151 TYR cc_start: 0.7700 (t80) cc_final: 0.6875 (m-80) REVERT: M 151 TYR cc_start: 0.7715 (t80) cc_final: 0.6866 (m-80) REVERT: O 151 TYR cc_start: 0.7707 (t80) cc_final: 0.6862 (m-80) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.4842 time to fit residues: 68.2825 Evaluate side-chains 128 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 33 optimal weight: 0.9980 chunk 137 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 GLN E 8 GLN G 8 GLN K 8 GLN O 8 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.111212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.092077 restraints weight = 13481.915| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.20 r_work: 0.2750 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 12544 Z= 0.113 Angle : 0.443 4.331 17144 Z= 0.241 Chirality : 0.044 0.131 2080 Planarity : 0.003 0.027 2120 Dihedral : 4.680 20.327 1896 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.21), residues: 1576 helix: 1.71 (0.19), residues: 704 sheet: 1.00 (0.23), residues: 248 loop : 0.32 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 5 TYR 0.008 0.001 TYR C 17 PHE 0.012 0.001 PHE C 78 TRP 0.002 0.001 TRP K 139 HIS 0.003 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (12544) covalent geometry : angle 0.44311 / 0.24 (17144) hydrogen bonds : bond 0.04098 / 2.76 ( 568) hydrogen bonds : angle 5.26248 / 3.81 ( 1704) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.455 Fit side-chains REVERT: A 151 TYR cc_start: 0.7574 (t80) cc_final: 0.6654 (m-80) REVERT: C 151 TYR cc_start: 0.7562 (t80) cc_final: 0.6646 (m-80) REVERT: E 151 TYR cc_start: 0.7565 (t80) cc_final: 0.6657 (m-80) REVERT: G 151 TYR cc_start: 0.7578 (t80) cc_final: 0.6667 (m-80) REVERT: I 151 TYR cc_start: 0.7571 (t80) cc_final: 0.6660 (m-80) REVERT: K 151 TYR cc_start: 0.7569 (t80) cc_final: 0.6664 (m-80) REVERT: M 151 TYR cc_start: 0.7584 (t80) cc_final: 0.6664 (m-80) REVERT: O 151 TYR cc_start: 0.7570 (t80) cc_final: 0.6654 (m-80) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.4319 time to fit residues: 62.1061 Evaluate side-chains 129 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 27 optimal weight: 10.0000 chunk 72 optimal weight: 0.2980 chunk 104 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 150 optimal weight: 0.9980 chunk 155 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN C 13 ASN E 13 ASN G 13 ASN I 13 ASN K 13 ASN M 8 GLN M 13 ASN O 13 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.108813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.092677 restraints weight = 13300.676| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 0.93 r_work: 0.2751 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9106 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 12544 Z= 0.202 Angle : 0.551 5.098 17144 Z= 0.291 Chirality : 0.049 0.148 2080 Planarity : 0.004 0.030 2120 Dihedral : 5.094 21.130 1896 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.21), residues: 1576 helix: 1.41 (0.19), residues: 704 sheet: 0.83 (0.24), residues: 248 loop : 0.10 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 169 TYR 0.010 0.002 TYR C 17 PHE 0.012 0.002 PHE C 78 TRP 0.003 0.001 TRP I 139 HIS 0.004 0.002 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (12544) covalent geometry : angle 0.55124 / 0.29 (17144) hydrogen bonds : bond 0.05164 / 3.47 ( 568) hydrogen bonds : angle 5.45948 / 3.95 ( 1704) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.404 Fit side-chains REVERT: A 151 TYR cc_start: 0.7731 (t80) cc_final: 0.6916 (m-80) REVERT: C 151 TYR cc_start: 0.7710 (t80) cc_final: 0.6889 (m-80) REVERT: E 151 TYR cc_start: 0.7735 (t80) cc_final: 0.6903 (m-80) REVERT: G 151 TYR cc_start: 0.7721 (t80) cc_final: 0.6906 (m-80) REVERT: I 151 TYR cc_start: 0.7729 (t80) cc_final: 0.6898 (m-80) REVERT: K 151 TYR cc_start: 0.7716 (t80) cc_final: 0.6911 (m-80) REVERT: M 151 TYR cc_start: 0.7725 (t80) cc_final: 0.6907 (m-80) REVERT: O 151 TYR cc_start: 0.7723 (t80) cc_final: 0.6897 (m-80) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.4815 time to fit residues: 66.1780 Evaluate side-chains 124 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 103 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 59 optimal weight: 0.2980 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 8 GLN E 13 ASN I 8 GLN M 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.109722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.093603 restraints weight = 13446.581| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 0.93 r_work: 0.2760 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12544 Z= 0.149 Angle : 0.491 5.124 17144 Z= 0.264 Chirality : 0.046 0.138 2080 Planarity : 0.004 0.029 2120 Dihedral : 4.887 20.687 1896 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.21), residues: 1576 helix: 1.46 (0.19), residues: 704 sheet: 0.75 (0.24), residues: 248 loop : 0.09 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 5 TYR 0.009 0.002 TYR I 17 PHE 0.012 0.002 PHE O 78 TRP 0.002 0.001 TRP C 139 HIS 0.004 0.001 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (12544) covalent geometry : angle 0.49147 / 0.26 (17144) hydrogen bonds : bond 0.04612 / 3.10 ( 568) hydrogen bonds : angle 5.36147 / 3.88 ( 1704) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.439 Fit side-chains REVERT: A 151 TYR cc_start: 0.7704 (t80) cc_final: 0.6877 (m-80) REVERT: C 151 TYR cc_start: 0.7687 (t80) cc_final: 0.6859 (m-80) REVERT: E 151 TYR cc_start: 0.7702 (t80) cc_final: 0.6870 (m-80) REVERT: G 151 TYR cc_start: 0.7706 (t80) cc_final: 0.6877 (m-80) REVERT: I 151 TYR cc_start: 0.7701 (t80) cc_final: 0.6871 (m-80) REVERT: K 151 TYR cc_start: 0.7695 (t80) cc_final: 0.6880 (m-80) REVERT: M 151 TYR cc_start: 0.7705 (t80) cc_final: 0.6873 (m-80) REVERT: O 151 TYR cc_start: 0.7698 (t80) cc_final: 0.6859 (m-80) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.4957 time to fit residues: 69.8052 Evaluate side-chains 128 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 GLN C 8 GLN E 8 GLN G 8 GLN I 8 GLN K 8 GLN M 8 GLN O 8 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.110188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.094096 restraints weight = 13390.705| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 0.92 r_work: 0.2771 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12544 Z= 0.139 Angle : 0.483 5.240 17144 Z= 0.260 Chirality : 0.046 0.136 2080 Planarity : 0.003 0.028 2120 Dihedral : 4.805 20.397 1896 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.72 % Allowed : 9.08 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.21), residues: 1576 helix: 1.50 (0.19), residues: 704 sheet: 0.64 (0.24), residues: 248 loop : 0.08 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 5 TYR 0.008 0.002 TYR I 17 PHE 0.012 0.002 PHE O 78 TRP 0.002 0.001 TRP C 139 HIS 0.003 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (12544) covalent geometry : angle 0.48299 / 0.26 (17144) hydrogen bonds : bond 0.04460 / 3.00 ( 568) hydrogen bonds : angle 5.32705 / 3.85 ( 1704) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.398 Fit side-chains REVERT: A 151 TYR cc_start: 0.7671 (t80) cc_final: 0.6853 (m-80) REVERT: C 151 TYR cc_start: 0.7648 (t80) cc_final: 0.6835 (m-80) REVERT: E 151 TYR cc_start: 0.7681 (t80) cc_final: 0.6865 (m-80) REVERT: G 151 TYR cc_start: 0.7673 (t80) cc_final: 0.6855 (m-80) REVERT: I 151 TYR cc_start: 0.7678 (t80) cc_final: 0.6863 (m-80) REVERT: K 151 TYR cc_start: 0.7660 (t80) cc_final: 0.6861 (m-80) REVERT: M 151 TYR cc_start: 0.7691 (t80) cc_final: 0.6875 (m-80) REVERT: O 151 TYR cc_start: 0.7669 (t80) cc_final: 0.6840 (m-80) outliers start: 8 outliers final: 0 residues processed: 133 average time/residue: 0.4513 time to fit residues: 66.6613 Evaluate side-chains 125 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 65 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 148 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 GLN E 8 GLN G 8 GLN K 8 GLN O 8 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.112238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.095028 restraints weight = 13370.299| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.03 r_work: 0.2783 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12544 Z= 0.098 Angle : 0.426 5.333 17144 Z= 0.235 Chirality : 0.044 0.126 2080 Planarity : 0.003 0.027 2120 Dihedral : 4.473 19.396 1896 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.22), residues: 1576 helix: 1.69 (0.20), residues: 704 sheet: 0.73 (0.24), residues: 248 loop : 0.20 (0.29), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 5 TYR 0.006 0.001 TYR I 17 PHE 0.012 0.001 PHE G 78 TRP 0.002 0.001 TRP K 139 HIS 0.002 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 (12544) covalent geometry : angle 0.42649 / 0.23 (17144) hydrogen bonds : bond 0.03750 / 2.52 ( 568) hydrogen bonds : angle 5.13797 / 3.72 ( 1704) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.495 Fit side-chains REVERT: A 151 TYR cc_start: 0.7722 (t80) cc_final: 0.6859 (m-80) REVERT: C 151 TYR cc_start: 0.7709 (t80) cc_final: 0.6848 (m-80) REVERT: E 151 TYR cc_start: 0.7698 (t80) cc_final: 0.6846 (m-80) REVERT: G 151 TYR cc_start: 0.7704 (t80) cc_final: 0.6855 (m-80) REVERT: I 151 TYR cc_start: 0.7706 (t80) cc_final: 0.6862 (m-80) REVERT: K 151 TYR cc_start: 0.7711 (t80) cc_final: 0.6860 (m-80) REVERT: M 151 TYR cc_start: 0.7718 (t80) cc_final: 0.6860 (m-80) REVERT: O 151 TYR cc_start: 0.7702 (t80) cc_final: 0.6847 (m-80) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.4894 time to fit residues: 67.7161 Evaluate side-chains 122 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 6 optimal weight: 0.0670 chunk 146 optimal weight: 0.0070 chunk 89 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 111 optimal weight: 0.0060 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 GLN E 8 GLN E 13 ASN G 8 GLN O 8 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.116949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.101537 restraints weight = 13191.913| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 0.90 r_work: 0.2906 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12544 Z= 0.078 Angle : 0.399 5.539 17144 Z= 0.220 Chirality : 0.042 0.120 2080 Planarity : 0.003 0.025 2120 Dihedral : 4.080 22.654 1896 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.22), residues: 1576 helix: 1.83 (0.20), residues: 712 sheet: 1.11 (0.24), residues: 248 loop : 0.52 (0.29), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 5 TYR 0.004 0.001 TYR E 17 PHE 0.011 0.001 PHE M 78 TRP 0.002 0.001 TRP C 197 HIS 0.001 0.000 HIS K 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00154 / 0.08 (12544) covalent geometry : angle 0.39910 / 0.22 (17144) hydrogen bonds : bond 0.02977 / 2.00 ( 568) hydrogen bonds : angle 4.82135 / 3.49 ( 1704) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3057.26 seconds wall clock time: 53 minutes 14.97 seconds (3194.97 seconds total)