Starting phenix.real_space_refine on Sat Jul 4 13:11:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mqf_23945/07_2026/7mqf_23945.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mqf_23945/07_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_23945/07_2026/7mqf_23945.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mqf_23945/07_2026/7mqf_23945.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mqf_23945/07_2026/7mqf_23945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mqf_23945/07_2026/7mqf_23945.map" model { file = "/net/cci-nas-00/data/ceres_data/7mqf_23945/07_2026/7mqf_23945.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mqf_23945/07_2026/7mqf_23945.cif" } 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-dev-6108/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: {'RNA': 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: 1.48, per 1000 atoms: 0.12 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: 0.78 Conformation dependent library (CDL) restraints added in 586.6 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: 0.30 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: 1.92 Time building geometry restraints manager: 1.16 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: 15514 1.13 - 2.25: 1390 2.25 - 3.38: 144 3.38 - 4.50: 61 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: 6808 15.04 - 30.08: 392 30.08 - 45.12: 104 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 - 0.028: 802 0.028 - 0.056: 625 0.056 - 0.084: 365 0.084 - 0.112: 201 0.112 - 0.140: 87 Chirality restraints: 2080 Sorted by residual: chirality pdb=" CA PRO A 63 " pdb=" N PRO A 63 " pdb=" C PRO A 63 " pdb=" CB PRO A 63 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA PRO C 63 " pdb=" N PRO C 63 " pdb=" C PRO C 63 " pdb=" CB PRO C 63 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA PRO I 63 " pdb=" N PRO I 63 " pdb=" C PRO I 63 " pdb=" CB PRO I 63 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.85e-01 ... (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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 9.950 Find NCS groups from input model: 0.120 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:8.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.810 ------------------------------------------------------------------------------- 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 : 0.716 5.625 17144 Z= 0.413 Chirality : 0.055 0.140 2080 Planarity : 0.004 0.025 2120 Dihedral : 11.725 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 0.71594 / 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 : 0.364 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: 0.5919 time to fit residues: 102.7139 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 : 0.584 ------------------------------------------------------------------------------- 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 = 0.3118 r_free = 0.3118 target = 0.110125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.090885 restraints weight = 13375.154| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.22 r_work: 0.2734 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.1148 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= 0.149 Angle : 0.517 4.700 17144 Z= 0.280 Chirality : 0.047 0.142 2080 Planarity : 0.004 0.025 2120 Dihedral : 6.294 39.970 1896 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 0.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % 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: 0.91 (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 M 78 TRP 0.003 0.001 TRP I 139 HIS 0.004 0.001 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (12544) covalent geometry : angle 0.51651 / 0.28 (17144) hydrogen bonds : bond 0.04786 / 3.22 ( 568) hydrogen bonds : angle 5.72862 / 4.14 ( 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 : 0.477 Fit side-chains REVERT: A 151 TYR cc_start: 0.7613 (t80) cc_final: 0.6617 (m-80) REVERT: C 151 TYR cc_start: 0.7592 (t80) cc_final: 0.6603 (m-80) REVERT: E 151 TYR cc_start: 0.7603 (t80) cc_final: 0.6621 (m-80) REVERT: G 151 TYR cc_start: 0.7606 (t80) cc_final: 0.6619 (m-80) REVERT: I 151 TYR cc_start: 0.7603 (t80) cc_final: 0.6604 (m-80) REVERT: K 151 TYR cc_start: 0.7614 (t80) cc_final: 0.6626 (m-80) REVERT: M 151 TYR cc_start: 0.7614 (t80) cc_final: 0.6615 (m-80) REVERT: O 151 TYR cc_start: 0.7600 (t80) cc_final: 0.6609 (m-80) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.6024 time to fit residues: 88.4913 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 : 0.449 ------------------------------------------------------------------------------- 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: 6.9990 chunk 88 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 105 optimal weight: 0.6980 chunk 73 optimal weight: 0.0270 chunk 81 optimal weight: 4.9990 chunk 159 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 overall best weight: 2.1442 ------------------------------------------------------------------------------- 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 = 0.3129 r_free = 0.3129 target = 0.109913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.094444 restraints weight = 13410.979| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 0.89 r_work: 0.2817 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9082 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 12544 Z= 0.135 Angle : 0.476 4.357 17144 Z= 0.258 Chirality : 0.046 0.138 2080 Planarity : 0.003 0.026 2120 Dihedral : 5.967 35.541 1896 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % 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: 1.74 (0.21), residues: 1576 helix: 1.84 (0.19), residues: 704 sheet: 0.92 (0.24), residues: 248 loop : 0.61 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 169 TYR 0.010 0.002 TYR K 17 PHE 0.012 0.002 PHE E 78 TRP 0.002 0.001 TRP C 139 HIS 0.003 0.001 HIS M 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (12544) covalent geometry : angle 0.47617 / 0.26 (17144) hydrogen bonds : bond 0.04508 / 3.03 ( 568) hydrogen bonds : angle 5.49619 / 3.98 ( 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 122 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.486 Fit side-chains REVERT: A 151 TYR cc_start: 0.7606 (t80) cc_final: 0.6785 (m-80) REVERT: C 151 TYR cc_start: 0.7586 (t80) cc_final: 0.6768 (m-80) REVERT: E 151 TYR cc_start: 0.7612 (t80) cc_final: 0.6790 (m-80) REVERT: G 151 TYR cc_start: 0.7617 (t80) cc_final: 0.6780 (m-80) REVERT: I 151 TYR cc_start: 0.7608 (t80) cc_final: 0.6788 (m-80) REVERT: K 151 TYR cc_start: 0.7609 (t80) cc_final: 0.6784 (m-80) REVERT: M 151 TYR cc_start: 0.7615 (t80) cc_final: 0.6790 (m-80) REVERT: O 151 TYR cc_start: 0.7611 (t80) cc_final: 0.6784 (m-80) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.4654 time to fit residues: 62.8307 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 : 0.360 ------------------------------------------------------------------------------- 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: 9.9990 chunk 75 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 9 optimal weight: 0.0370 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 overall best weight: 4.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.108133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.090832 restraints weight = 13362.749| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 1.03 r_work: 0.2719 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.1460 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= 0.217 Angle : 0.561 5.505 17144 Z= 0.297 Chirality : 0.049 0.151 2080 Planarity : 0.004 0.030 2120 Dihedral : 6.388 34.816 1896 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % 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: 1.30 (0.21), residues: 1576 helix: 1.49 (0.19), residues: 704 sheet: 0.92 (0.23), residues: 248 loop : 0.23 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 169 TYR 0.012 0.003 TYR K 17 PHE 0.013 0.002 PHE C 78 TRP 0.003 0.001 TRP I 139 HIS 0.005 0.002 HIS E 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 (12544) covalent geometry : angle 0.56066 / 0.30 (17144) hydrogen bonds : bond 0.05412 / 3.64 ( 568) hydrogen bonds : angle 5.59047 / 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 128 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.365 Fit side-chains REVERT: A 151 TYR cc_start: 0.7796 (t80) cc_final: 0.6906 (m-80) REVERT: C 151 TYR cc_start: 0.7788 (t80) cc_final: 0.6903 (m-80) REVERT: E 151 TYR cc_start: 0.7783 (t80) cc_final: 0.6895 (m-80) REVERT: G 151 TYR cc_start: 0.7797 (t80) cc_final: 0.6908 (m-80) REVERT: I 151 TYR cc_start: 0.7793 (t80) cc_final: 0.6898 (m-80) REVERT: K 151 TYR cc_start: 0.7785 (t80) cc_final: 0.6898 (m-80) REVERT: M 151 TYR cc_start: 0.7792 (t80) cc_final: 0.6902 (m-80) REVERT: O 151 TYR cc_start: 0.7786 (t80) cc_final: 0.6898 (m-80) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.4700 time to fit residues: 66.3870 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 : 0.292 ------------------------------------------------------------------------------- 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: 5.9990 chunk 61 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.107751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.090455 restraints weight = 13434.377| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 1.02 r_work: 0.2714 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9127 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 12544 Z= 0.254 Angle : 0.596 6.159 17144 Z= 0.314 Chirality : 0.051 0.156 2080 Planarity : 0.005 0.031 2120 Dihedral : 6.729 39.112 1896 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % 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: 0.84 (0.21), residues: 1576 helix: 1.15 (0.19), residues: 704 sheet: 0.80 (0.23), residues: 248 loop : -0.12 (0.27), 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 0.013 0.002 PHE C 78 TRP 0.004 0.002 TRP E 139 HIS 0.005 0.002 HIS M 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.25 (12544) covalent geometry : angle 0.59619 / 0.31 (17144) hydrogen bonds : bond 0.05692 / 3.83 ( 568) hydrogen bonds : angle 5.61592 / 4.06 ( 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 : 0.477 Fit side-chains REVERT: A 151 TYR cc_start: 0.7801 (t80) cc_final: 0.6949 (m-80) REVERT: C 151 TYR cc_start: 0.7789 (t80) cc_final: 0.6911 (m-80) REVERT: E 151 TYR cc_start: 0.7799 (t80) cc_final: 0.6919 (m-80) REVERT: G 151 TYR cc_start: 0.7805 (t80) cc_final: 0.6926 (m-80) REVERT: I 151 TYR cc_start: 0.7796 (t80) cc_final: 0.6924 (m-80) REVERT: K 151 TYR cc_start: 0.7784 (t80) cc_final: 0.6936 (m-80) REVERT: M 151 TYR cc_start: 0.7801 (t80) cc_final: 0.6939 (m-80) REVERT: O 151 TYR cc_start: 0.7790 (t80) cc_final: 0.6935 (m-80) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.4387 time to fit residues: 61.9952 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 : 0.463 ------------------------------------------------------------------------------- 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: 10.0000 chunk 137 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 GLN C 8 GLN E 8 GLN G 8 GLN K 8 GLN M 8 GLN O 8 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.109578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.093425 restraints weight = 13469.467| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 0.93 r_work: 0.2759 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9103 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 12544 Z= 0.155 Angle : 0.487 4.436 17144 Z= 0.263 Chirality : 0.046 0.138 2080 Planarity : 0.004 0.029 2120 Dihedral : 6.271 34.297 1896 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.02 (0.21), residues: 1576 helix: 1.38 (0.19), residues: 704 sheet: 0.71 (0.23), residues: 248 loop : -0.04 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 5 TYR 0.009 0.002 TYR I 17 PHE 0.012 0.002 PHE G 78 TRP 0.002 0.001 TRP C 139 HIS 0.004 0.001 HIS M 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (12544) covalent geometry : angle 0.48721 / 0.26 (17144) hydrogen bonds : bond 0.04677 / 3.15 ( 568) hydrogen bonds : angle 5.42274 / 3.92 ( 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 128 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.311 Fit side-chains REVERT: A 151 TYR cc_start: 0.7703 (t80) cc_final: 0.6874 (m-80) REVERT: C 151 TYR cc_start: 0.7695 (t80) cc_final: 0.6862 (m-80) REVERT: E 151 TYR cc_start: 0.7712 (t80) cc_final: 0.6881 (m-80) REVERT: G 151 TYR cc_start: 0.7705 (t80) cc_final: 0.6887 (m-80) REVERT: I 151 TYR cc_start: 0.7708 (t80) cc_final: 0.6886 (m-80) REVERT: K 151 TYR cc_start: 0.7687 (t80) cc_final: 0.6870 (m-80) REVERT: M 151 TYR cc_start: 0.7698 (t80) cc_final: 0.6869 (m-80) REVERT: O 151 TYR cc_start: 0.7697 (t80) cc_final: 0.6861 (m-80) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.4604 time to fit residues: 64.8740 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 : 0.460 ------------------------------------------------------------------------------- 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: 8.9990 chunk 104 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 150 optimal weight: 0.5980 chunk 155 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3124 r_free = 0.3124 target = 0.110745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.093291 restraints weight = 13321.740| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.04 r_work: 0.2768 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 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 0.018 12544 Z= 0.118 Angle : 0.446 4.347 17144 Z= 0.245 Chirality : 0.044 0.131 2080 Planarity : 0.003 0.027 2120 Dihedral : 5.936 34.617 1896 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.72 % Allowed : 9.26 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.20 (0.21), residues: 1576 helix: 1.56 (0.19), residues: 704 sheet: 0.68 (0.23), residues: 248 loop : 0.08 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 5 TYR 0.008 0.001 TYR I 17 PHE 0.012 0.002 PHE G 78 TRP 0.002 0.001 TRP C 139 HIS 0.003 0.001 HIS E 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (12544) covalent geometry : angle 0.44605 / 0.24 (17144) hydrogen bonds : bond 0.04177 / 2.81 ( 568) hydrogen bonds : angle 5.29599 / 3.83 ( 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 144 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.316 Fit side-chains REVERT: A 151 TYR cc_start: 0.7615 (t80) cc_final: 0.6744 (m-80) REVERT: C 151 TYR cc_start: 0.7612 (t80) cc_final: 0.6734 (m-80) REVERT: E 151 TYR cc_start: 0.7599 (t80) cc_final: 0.6738 (m-80) REVERT: G 151 TYR cc_start: 0.7599 (t80) cc_final: 0.6748 (m-80) REVERT: I 151 TYR cc_start: 0.7603 (t80) cc_final: 0.6742 (m-80) REVERT: K 151 TYR cc_start: 0.7613 (t80) cc_final: 0.6753 (m-80) REVERT: M 151 TYR cc_start: 0.7623 (t80) cc_final: 0.6745 (m-80) REVERT: O 151 TYR cc_start: 0.7614 (t80) cc_final: 0.6743 (m-80) outliers start: 8 outliers final: 0 residues processed: 144 average time/residue: 0.4476 time to fit residues: 71.3931 Evaluate side-chains 136 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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: 4.9990 chunk 36 optimal weight: 4.9990 chunk 59 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 1 optimal weight: 0.0060 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 GLN A 13 ASN C 8 GLN C 13 ASN E 13 ASN G 8 GLN G 13 ASN I 8 GLN I 13 ASN K 8 GLN K 13 ASN M 8 GLN M 13 ASN O 13 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.111587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.095996 restraints weight = 13448.358| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 0.90 r_work: 0.2801 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12544 Z= 0.103 Angle : 0.431 4.894 17144 Z= 0.238 Chirality : 0.044 0.128 2080 Planarity : 0.003 0.026 2120 Dihedral : 5.813 34.775 1896 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.35 (0.22), residues: 1576 helix: 1.68 (0.20), residues: 704 sheet: 0.74 (0.24), residues: 248 loop : 0.15 (0.29), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 5 TYR 0.006 0.001 TYR M 17 PHE 0.012 0.001 PHE C 78 TRP 0.002 0.001 TRP A 139 HIS 0.002 0.001 HIS O 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (12544) covalent geometry : angle 0.43132 / 0.24 (17144) hydrogen bonds : bond 0.03883 / 2.61 ( 568) hydrogen bonds : angle 5.18719 / 3.75 ( 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 136 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.488 Fit side-chains REVERT: A 151 TYR cc_start: 0.7691 (t80) cc_final: 0.6884 (m-80) REVERT: C 151 TYR cc_start: 0.7676 (t80) cc_final: 0.6867 (m-80) REVERT: E 151 TYR cc_start: 0.7676 (t80) cc_final: 0.6874 (m-80) REVERT: G 151 TYR cc_start: 0.7679 (t80) cc_final: 0.6879 (m-80) REVERT: I 151 TYR cc_start: 0.7679 (t80) cc_final: 0.6877 (m-80) REVERT: K 151 TYR cc_start: 0.7680 (t80) cc_final: 0.6879 (m-80) REVERT: M 151 TYR cc_start: 0.7687 (t80) cc_final: 0.6878 (m-80) REVERT: O 151 TYR cc_start: 0.7678 (t80) cc_final: 0.6868 (m-80) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.4770 time to fit residues: 71.5825 Evaluate side-chains 136 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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: 10.0000 chunk 152 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 133 optimal weight: 0.4980 chunk 142 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 overall best weight: 2.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 GLN A 13 ASN C 8 GLN C 13 ASN E 8 GLN E 13 ASN G 8 GLN G 13 ASN I 8 GLN I 13 ASN K 8 GLN K 13 ASN M 8 GLN M 13 ASN O 8 GLN O 13 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.110393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.093284 restraints weight = 13381.289| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.01 r_work: 0.2756 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12544 Z= 0.132 Angle : 0.473 5.625 17144 Z= 0.257 Chirality : 0.045 0.135 2080 Planarity : 0.003 0.027 2120 Dihedral : 5.949 34.763 1896 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.58 (0.19), residues: 704 sheet: 0.66 (0.24), residues: 248 loop : 0.14 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 169 TYR 0.008 0.002 TYR I 17 PHE 0.012 0.002 PHE C 78 TRP 0.002 0.001 TRP A 139 HIS 0.003 0.001 HIS E 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (12544) covalent geometry : angle 0.47298 / 0.26 (17144) hydrogen bonds : bond 0.04360 / 2.93 ( 568) hydrogen bonds : angle 5.26986 / 3.81 ( 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 127 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.484 Fit side-chains REVERT: A 151 TYR cc_start: 0.7721 (t80) cc_final: 0.6884 (m-80) REVERT: C 151 TYR cc_start: 0.7703 (t80) cc_final: 0.6856 (m-80) REVERT: E 151 TYR cc_start: 0.7704 (t80) cc_final: 0.6865 (m-80) REVERT: G 151 TYR cc_start: 0.7713 (t80) cc_final: 0.6880 (m-80) REVERT: I 151 TYR cc_start: 0.7723 (t80) cc_final: 0.6882 (m-80) REVERT: K 151 TYR cc_start: 0.7707 (t80) cc_final: 0.6866 (m-80) REVERT: M 151 TYR cc_start: 0.7746 (t80) cc_final: 0.6886 (m-80) REVERT: O 151 TYR cc_start: 0.7720 (t80) cc_final: 0.6872 (m-80) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.5091 time to fit residues: 71.3112 Evaluate side-chains 127 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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: 10.0000 chunk 60 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 148 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.111116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.093811 restraints weight = 13343.093| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.03 r_work: 0.2756 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12544 Z= 0.113 Angle : 0.452 6.380 17144 Z= 0.249 Chirality : 0.044 0.130 2080 Planarity : 0.003 0.027 2120 Dihedral : 5.844 34.788 1896 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.33 (0.22), residues: 1576 helix: 1.66 (0.20), residues: 704 sheet: 0.66 (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 0.007 0.001 TYR I 17 PHE 0.012 0.002 PHE M 78 TRP 0.002 0.001 TRP O 139 HIS 0.003 0.001 HIS E 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (12544) covalent geometry : angle 0.45233 / 0.25 (17144) hydrogen bonds : bond 0.04038 / 2.72 ( 568) hydrogen bonds : angle 5.20118 / 3.76 ( 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 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: 0.7791 (t80) cc_final: 0.6940 (m-80) REVERT: C 151 TYR cc_start: 0.7777 (t80) cc_final: 0.6912 (m-80) REVERT: E 151 TYR cc_start: 0.7747 (t80) cc_final: 0.6902 (m-80) REVERT: G 151 TYR cc_start: 0.7750 (t80) cc_final: 0.6906 (m-80) REVERT: I 151 TYR cc_start: 0.7771 (t80) cc_final: 0.6913 (m-80) REVERT: K 151 TYR cc_start: 0.7745 (t80) cc_final: 0.6908 (m-80) REVERT: M 151 TYR cc_start: 0.7781 (t80) cc_final: 0.6921 (m-80) REVERT: O 151 TYR cc_start: 0.7770 (t80) cc_final: 0.6908 (m-80) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.5048 time to fit residues: 75.3749 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 : 0.491 ------------------------------------------------------------------------------- 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: 7.9990 chunk 146 optimal weight: 0.1980 chunk 89 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 GLN A 13 ASN C 13 ASN E 8 GLN E 13 ASN G 8 GLN G 13 ASN I 8 GLN I 13 ASN K 8 GLN K 13 ASN M 8 GLN M 13 ASN O 8 GLN O 13 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.109403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.093510 restraints weight = 13274.591| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 0.91 r_work: 0.2762 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9105 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12544 Z= 0.177 Angle : 0.529 6.314 17144 Z= 0.283 Chirality : 0.047 0.143 2080 Planarity : 0.004 0.028 2120 Dihedral : 6.161 34.751 1896 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % 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: 1.07 (0.21), residues: 1576 helix: 1.43 (0.19), residues: 704 sheet: 0.59 (0.24), residues: 248 loop : 0.04 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 169 TYR 0.009 0.002 TYR I 17 PHE 0.011 0.002 PHE C 78 TRP 0.003 0.001 TRP K 139 HIS 0.004 0.001 HIS E 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (12544) covalent geometry : angle 0.52873 / 0.28 (17144) hydrogen bonds : bond 0.04873 / 3.28 ( 568) hydrogen bonds : angle 5.38254 / 3.89 ( 1704) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3175.06 seconds wall clock time: 55 minutes 0.15 seconds (3300.15 seconds total)