Starting phenix.real_space_refine on Tue Aug 4 23:36:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vt4_65314/08_2026/9vt4_65314.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vt4_65314/08_2026/9vt4_65314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vt4_65314/08_2026/9vt4_65314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vt4_65314/08_2026/9vt4_65314.map" model { file = "/net/cci-nas-00/data/ceres_data/9vt4_65314/08_2026/9vt4_65314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vt4_65314/08_2026/9vt4_65314.cif" } resolution = 2.96 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= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4797 2.51 5 N 1275 2.21 5 O 1389 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7494 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1045 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 723 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 90} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 702 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 1, 'TRANS': 96} Chain breaks: 3 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 3, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: C, E, D, F, H, I, K, L Time building chain proxies: 1.25, per 1000 atoms: 0.17 Number of scatterers: 7494 At special positions: 0 Unit cell: (111.52, 111.52, 72.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1389 8.00 N 1275 7.00 C 4797 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 98 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 135 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 98 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG J 1 " - " ASN B 563 " " NAG K 1 " - " ASN D 563 " " NAG L 1 " - " ASN F 563 " Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 282.8 milliseconds 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1794 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 18 sheets defined 17.4% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 85 Processing helix chain 'B' and resid 554 through 576 removed outlier: 3.756A pdb=" N GLN B 560 " --> pdb=" O CYS B 556 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLN B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 597 removed outlier: 3.547A pdb=" N ARG B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 31 Processing helix chain 'G' and resid 64 through 67 removed outlier: 3.524A pdb=" N LYS G 67 " --> pdb=" O ASP G 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 64 through 67' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 85 Processing helix chain 'D' and resid 554 through 576 removed outlier: 3.756A pdb=" N GLN D 560 " --> pdb=" O CYS D 556 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 597 removed outlier: 3.547A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 64 through 67 removed outlier: 3.524A pdb=" N LYS H 67 " --> pdb=" O ASP H 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 64 through 67' Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 78 through 85 Processing helix chain 'F' and resid 554 through 576 removed outlier: 3.757A pdb=" N GLN F 560 " --> pdb=" O CYS F 556 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 597 removed outlier: 3.547A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 31 Processing helix chain 'I' and resid 64 through 67 removed outlier: 3.524A pdb=" N LYS I 67 " --> pdb=" O ASP I 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 64 through 67' Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.555A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 69 removed outlier: 6.823A pdb=" N VAL A 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA4, first strand: chain 'B' and resid 518 through 520 Processing sheet with id=AA5, first strand: chain 'G' and resid 2 through 6 Processing sheet with id=AA6, first strand: chain 'G' and resid 60 through 62 removed outlier: 6.551A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.555A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 63 through 69 removed outlier: 6.822A pdb=" N VAL C 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AB1, first strand: chain 'D' and resid 518 through 520 Processing sheet with id=AB2, first strand: chain 'H' and resid 2 through 6 Processing sheet with id=AB3, first strand: chain 'H' and resid 60 through 62 removed outlier: 6.551A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 36 through 37 removed outlier: 6.555A pdb=" N CYS E 108 " --> pdb=" O HIS E 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 63 through 69 removed outlier: 6.822A pdb=" N VAL E 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 86 through 89 Processing sheet with id=AB7, first strand: chain 'F' and resid 518 through 520 Processing sheet with id=AB8, first strand: chain 'I' and resid 2 through 6 Processing sheet with id=AB9, first strand: chain 'I' and resid 60 through 62 removed outlier: 6.551A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) 237 hydrogen bonds defined for protein. 612 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: 1.11 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1239 1.32 - 1.44: 2231 1.44 - 1.56: 4162 1.56 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 7674 Sorted by residual: bond pdb=" CA ALA A 166 " pdb=" C ALA A 166 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.22e-02 6.72e+03 1.63e+01 bond pdb=" CA ALA C 166 " pdb=" C ALA C 166 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.22e-02 6.72e+03 1.61e+01 bond pdb=" CA ALA E 166 " pdb=" C ALA E 166 " ideal model delta sigma weight residual 1.524 1.476 0.049 1.22e-02 6.72e+03 1.58e+01 bond pdb=" CA PHE E 160 " pdb=" CB PHE E 160 " ideal model delta sigma weight residual 1.527 1.478 0.049 1.30e-02 5.92e+03 1.42e+01 bond pdb=" CA PHE A 160 " pdb=" CB PHE A 160 " ideal model delta sigma weight residual 1.527 1.478 0.049 1.30e-02 5.92e+03 1.41e+01 ... (remaining 7669 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 10114 1.45 - 2.90: 277 2.90 - 4.36: 40 4.36 - 5.81: 18 5.81 - 7.26: 3 Bond angle restraints: 10452 Sorted by residual: angle pdb=" N PHE A 159 " pdb=" CA PHE A 159 " pdb=" C PHE A 159 " ideal model delta sigma weight residual 110.14 105.89 4.25 1.55e+00 4.16e-01 7.50e+00 angle pdb=" N PHE C 159 " pdb=" CA PHE C 159 " pdb=" C PHE C 159 " ideal model delta sigma weight residual 110.14 105.90 4.24 1.55e+00 4.16e-01 7.48e+00 angle pdb=" N PHE E 159 " pdb=" CA PHE E 159 " pdb=" C PHE E 159 " ideal model delta sigma weight residual 110.14 105.93 4.21 1.55e+00 4.16e-01 7.36e+00 angle pdb=" C TYR C 99 " pdb=" CA TYR C 99 " pdb=" CB TYR C 99 " ideal model delta sigma weight residual 109.65 114.24 -4.59 1.75e+00 3.27e-01 6.89e+00 angle pdb=" C TYR E 99 " pdb=" CA TYR E 99 " pdb=" CB TYR E 99 " ideal model delta sigma weight residual 109.65 114.22 -4.57 1.75e+00 3.27e-01 6.83e+00 ... (remaining 10447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 4113 17.74 - 35.48: 309 35.48 - 53.22: 45 53.22 - 70.96: 12 70.96 - 88.70: 6 Dihedral angle restraints: 4485 sinusoidal: 1665 harmonic: 2820 Sorted by residual: dihedral pdb=" CB CYS F 511 " pdb=" SG CYS F 511 " pdb=" SG CYS F 556 " pdb=" CB CYS F 556 " ideal model delta sinusoidal sigma weight residual -86.00 -115.00 29.00 1 1.00e+01 1.00e-02 1.20e+01 dihedral pdb=" CB CYS B 511 " pdb=" SG CYS B 511 " pdb=" SG CYS B 556 " pdb=" CB CYS B 556 " ideal model delta sinusoidal sigma weight residual -86.00 -114.99 28.99 1 1.00e+01 1.00e-02 1.20e+01 dihedral pdb=" CB CYS D 511 " pdb=" SG CYS D 511 " pdb=" SG CYS D 556 " pdb=" CB CYS D 556 " ideal model delta sinusoidal sigma weight residual -86.00 -114.95 28.95 1 1.00e+01 1.00e-02 1.20e+01 ... (remaining 4482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 906 0.045 - 0.089: 187 0.089 - 0.134: 73 0.134 - 0.179: 4 0.179 - 0.224: 3 Chirality restraints: 1173 Sorted by residual: chirality pdb=" CA ARG E 164 " pdb=" N ARG E 164 " pdb=" C ARG E 164 " pdb=" CB ARG E 164 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ARG C 164 " pdb=" N ARG C 164 " pdb=" C ARG C 164 " pdb=" CB ARG C 164 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ARG A 164 " pdb=" N ARG A 164 " pdb=" C ARG A 164 " pdb=" CB ARG A 164 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1170 not shown) Planarity restraints: 1332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 125 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO E 126 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 126 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 126 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 125 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 126 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 125 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.46e+00 pdb=" N PRO C 126 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 126 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 126 " -0.017 5.00e-02 4.00e+02 ... (remaining 1329 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2440 2.83 - 3.35: 6419 3.35 - 3.86: 13115 3.86 - 4.38: 15237 4.38 - 4.90: 26467 Nonbonded interactions: 63678 Sorted by model distance: nonbonded pdb=" OH TYR C 99 " pdb=" O TYR C 162 " model vdw 2.310 3.040 nonbonded pdb=" OH TYR E 99 " pdb=" O TYR E 162 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR A 99 " pdb=" O TYR A 162 " model vdw 2.311 3.040 nonbonded pdb=" O ASP A 127 " pdb=" NH2 ARG B 580 " model vdw 2.378 3.120 nonbonded pdb=" O ASP C 127 " pdb=" NH2 ARG D 580 " model vdw 2.378 3.120 ... (remaining 63673 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 6.630 Find NCS groups from input model: 0.060 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:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.004 0.049 7689 Z= 0.277 Angle : 0.595 7.261 10488 Z= 0.317 Chirality : 0.044 0.224 1173 Planarity : 0.004 0.030 1329 Dihedral : 12.969 88.698 2664 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 12.80 % Favored : 87.20 % 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: -0.64 (0.26), residues: 957 helix: 0.87 (0.43), residues: 162 sheet: -0.99 (0.37), residues: 183 loop : -0.57 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 164 TYR 0.011 0.001 TYR C 99 PHE 0.011 0.001 PHE C 159 TRP 0.011 0.001 TRP E 104 HIS 0.002 0.001 HIS D 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.28 ( 7674) covalent geometry : angle 0.59190 / 0.32 (10452) SS BOND : bond 0.00192 / 0.12 ( 9) SS BOND : angle 0.76165 / 0.50 ( 18) hydrogen bonds : bond 0.12936 / 8.89 ( 237) hydrogen bonds : angle 6.03301 / 4.37 ( 612) link_BETA1-4 : bond 0.00055 / 0.03 ( 3) link_BETA1-4 : angle 1.41427 / 0.72 ( 9) link_NAG-ASN : bond 0.00098 / 0.05 ( 3) link_NAG-ASN : angle 1.76195 / 0.98 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.186 Fit side-chains REVERT: G 30 SER cc_start: 0.8308 (t) cc_final: 0.8028 (p) REVERT: H 30 SER cc_start: 0.8359 (t) cc_final: 0.8043 (p) REVERT: H 122 THR cc_start: 0.8221 (p) cc_final: 0.7974 (p) REVERT: I 122 THR cc_start: 0.8213 (p) cc_final: 0.8007 (p) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.3242 time to fit residues: 45.6379 Evaluate side-chains 87 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 ASN ** B 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.158757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121547 restraints weight = 8046.701| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.06 r_work: 0.3106 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7689 Z= 0.192 Angle : 0.550 5.246 10488 Z= 0.280 Chirality : 0.044 0.161 1173 Planarity : 0.004 0.027 1329 Dihedral : 4.263 26.040 1197 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.67 % Allowed : 16.60 % Favored : 80.73 % 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: -0.85 (0.25), residues: 957 helix: 0.53 (0.43), residues: 162 sheet: -1.02 (0.36), residues: 213 loop : -0.66 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 130 TYR 0.021 0.001 TYR D 543 PHE 0.009 0.001 PHE C 176 TRP 0.006 0.001 TRP G 118 HIS 0.006 0.002 HIS E 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 7674) covalent geometry : angle 0.54401 / 0.28 (10452) SS BOND : bond 0.00154 / 0.09 ( 9) SS BOND : angle 0.45688 / 0.30 ( 18) hydrogen bonds : bond 0.03817 / 2.57 ( 237) hydrogen bonds : angle 5.00029 / 3.71 ( 612) link_BETA1-4 : bond 0.00138 / 0.07 ( 3) link_BETA1-4 : angle 2.16891 / 1.11 ( 9) link_NAG-ASN : bond 0.00213 / 0.10 ( 3) link_NAG-ASN : angle 1.79765 / 1.03 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.187 Fit side-chains REVERT: G 31 ILE cc_start: 0.8183 (mt) cc_final: 0.7950 (mm) REVERT: D 545 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.6727 (mp0) REVERT: D 580 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8373 (mtm-85) REVERT: H 122 THR cc_start: 0.8124 (p) cc_final: 0.7800 (p) REVERT: I 122 THR cc_start: 0.8015 (p) cc_final: 0.7783 (p) outliers start: 19 outliers final: 11 residues processed: 99 average time/residue: 0.3201 time to fit residues: 34.4248 Evaluate side-chains 93 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 580 ARG Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 41 optimal weight: 0.0570 chunk 50 optimal weight: 7.9990 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 550 ASN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.158819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.121889 restraints weight = 7959.545| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.04 r_work: 0.3112 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 : 0.003 0.026 7689 Z= 0.145 Angle : 0.495 4.995 10488 Z= 0.252 Chirality : 0.043 0.153 1173 Planarity : 0.003 0.025 1329 Dihedral : 3.954 15.869 1197 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.38 % Allowed : 17.58 % Favored : 79.04 % 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: -0.78 (0.26), residues: 957 helix: 0.51 (0.43), residues: 162 sheet: -0.90 (0.36), residues: 213 loop : -0.61 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 130 TYR 0.012 0.001 TYR D 543 PHE 0.007 0.001 PHE C 176 TRP 0.006 0.001 TRP I 104 HIS 0.002 0.001 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 7674) covalent geometry : angle 0.49033 / 0.25 (10452) SS BOND : bond 0.00097 / 0.06 ( 9) SS BOND : angle 0.34638 / 0.22 ( 18) hydrogen bonds : bond 0.03502 / 2.37 ( 237) hydrogen bonds : angle 4.73583 / 3.50 ( 612) link_BETA1-4 : bond 0.00063 / 0.03 ( 3) link_BETA1-4 : angle 1.84574 / 0.94 ( 9) link_NAG-ASN : bond 0.00111 / 0.06 ( 3) link_NAG-ASN : angle 1.49266 / 0.85 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.159 Fit side-chains REVERT: B 580 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8284 (mtm-85) REVERT: G 31 ILE cc_start: 0.8184 (mt) cc_final: 0.7976 (mm) REVERT: D 580 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8385 (mtm-85) REVERT: H 122 THR cc_start: 0.8103 (p) cc_final: 0.7772 (p) REVERT: I 21 SER cc_start: 0.8034 (OUTLIER) cc_final: 0.7468 (t) REVERT: I 122 THR cc_start: 0.7991 (p) cc_final: 0.7751 (p) outliers start: 24 outliers final: 11 residues processed: 100 average time/residue: 0.3263 time to fit residues: 35.2789 Evaluate side-chains 94 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 580 ARG Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain D residue 580 ARG Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 108 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 89 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 83 optimal weight: 0.2980 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 514 ASN ** B 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 550 ASN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.159325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122440 restraints weight = 8082.150| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.05 r_work: 0.3148 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7689 Z= 0.123 Angle : 0.474 4.947 10488 Z= 0.241 Chirality : 0.042 0.153 1173 Planarity : 0.003 0.025 1329 Dihedral : 3.777 11.786 1197 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.50 % Allowed : 16.32 % Favored : 79.18 % 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: -0.80 (0.26), residues: 957 helix: 0.55 (0.43), residues: 162 sheet: -1.17 (0.35), residues: 234 loop : -0.48 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 130 TYR 0.011 0.001 TYR G 105 PHE 0.007 0.001 PHE C 176 TRP 0.006 0.001 TRP I 104 HIS 0.002 0.001 HIS E 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 7674) covalent geometry : angle 0.47060 / 0.24 (10452) SS BOND : bond 0.00041 / 0.03 ( 9) SS BOND : angle 0.22448 / 0.14 ( 18) hydrogen bonds : bond 0.03228 / 2.19 ( 237) hydrogen bonds : angle 4.57677 / 3.38 ( 612) link_BETA1-4 : bond 0.00042 / 0.02 ( 3) link_BETA1-4 : angle 1.73461 / 0.88 ( 9) link_NAG-ASN : bond 0.00043 / 0.02 ( 3) link_NAG-ASN : angle 1.37963 / 0.78 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 0.201 Fit side-chains REVERT: B 580 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8310 (mtm-85) REVERT: C 77 THR cc_start: 0.8442 (p) cc_final: 0.7977 (t) REVERT: C 156 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8401 (mt-10) REVERT: D 545 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.6595 (mp0) REVERT: D 580 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8363 (mtm-85) REVERT: H 122 THR cc_start: 0.8064 (p) cc_final: 0.7729 (p) REVERT: I 21 SER cc_start: 0.8013 (OUTLIER) cc_final: 0.7465 (t) REVERT: I 122 THR cc_start: 0.7991 (p) cc_final: 0.7748 (p) outliers start: 32 outliers final: 16 residues processed: 111 average time/residue: 0.3107 time to fit residues: 37.6130 Evaluate side-chains 102 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 514 ASN Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 580 ARG Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 580 ARG Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain F residue 574 ARG Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 65 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 15 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 76 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 550 ASN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.160094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.123136 restraints weight = 7995.040| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.04 r_work: 0.3159 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7689 Z= 0.111 Angle : 0.469 4.898 10488 Z= 0.239 Chirality : 0.042 0.152 1173 Planarity : 0.003 0.025 1329 Dihedral : 3.710 12.250 1197 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.80 % Allowed : 17.30 % Favored : 78.90 % 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: -0.80 (0.26), residues: 957 helix: 0.57 (0.43), residues: 159 sheet: -1.13 (0.35), residues: 234 loop : -0.51 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 130 TYR 0.011 0.001 TYR G 105 PHE 0.006 0.001 PHE C 176 TRP 0.006 0.001 TRP I 104 HIS 0.002 0.001 HIS E 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 7674) covalent geometry : angle 0.46580 / 0.24 (10452) SS BOND : bond 0.00177 / 0.12 ( 9) SS BOND : angle 0.33161 / 0.22 ( 18) hydrogen bonds : bond 0.03088 / 2.10 ( 237) hydrogen bonds : angle 4.48011 / 3.30 ( 612) link_BETA1-4 : bond 0.00082 / 0.04 ( 3) link_BETA1-4 : angle 1.62378 / 0.83 ( 9) link_NAG-ASN : bond 0.00016 / 0.01 ( 3) link_NAG-ASN : angle 1.33006 / 0.75 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.283 Fit side-chains REVERT: C 77 THR cc_start: 0.8446 (p) cc_final: 0.8014 (t) REVERT: C 156 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8399 (mt-10) REVERT: D 545 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.6404 (mp0) REVERT: D 580 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8282 (mtm-85) REVERT: H 122 THR cc_start: 0.8054 (p) cc_final: 0.7724 (p) REVERT: I 122 THR cc_start: 0.7960 (p) cc_final: 0.7716 (p) outliers start: 27 outliers final: 16 residues processed: 102 average time/residue: 0.3564 time to fit residues: 39.6845 Evaluate side-chains 96 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 580 ARG Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 108 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 41 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 550 ASN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.153174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.115157 restraints weight = 8123.467| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.07 r_work: 0.3021 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 7689 Z= 0.296 Angle : 0.615 5.342 10488 Z= 0.312 Chirality : 0.047 0.157 1173 Planarity : 0.004 0.023 1329 Dihedral : 4.388 14.262 1197 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.64 % Allowed : 16.17 % Favored : 79.18 % 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: -1.22 (0.25), residues: 957 helix: -0.24 (0.40), residues: 162 sheet: -1.05 (0.35), residues: 219 loop : -0.83 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 134 TYR 0.017 0.002 TYR G 105 PHE 0.012 0.002 PHE B 592 TRP 0.012 0.002 TRP G 36 HIS 0.003 0.001 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.30 ( 7674) covalent geometry : angle 0.60900 / 0.31 (10452) SS BOND : bond 0.00289 / 0.19 ( 9) SS BOND : angle 0.59573 / 0.34 ( 18) hydrogen bonds : bond 0.04165 / 2.76 ( 237) hydrogen bonds : angle 5.12053 / 3.74 ( 612) link_BETA1-4 : bond 0.00221 / 0.11 ( 3) link_BETA1-4 : angle 2.51747 / 1.26 ( 9) link_NAG-ASN : bond 0.00284 / 0.14 ( 3) link_NAG-ASN : angle 1.61004 / 0.92 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.332 Fit side-chains REVERT: B 580 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8290 (mtm-85) REVERT: G 31 ILE cc_start: 0.8188 (mt) cc_final: 0.7923 (mm) REVERT: C 156 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8469 (mt-10) REVERT: D 543 TYR cc_start: 0.8635 (m-80) cc_final: 0.8363 (m-80) REVERT: D 545 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.6907 (mp0) REVERT: D 580 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8350 (mtm-85) REVERT: H 122 THR cc_start: 0.8009 (p) cc_final: 0.7713 (p) REVERT: I 122 THR cc_start: 0.8097 (p) cc_final: 0.7827 (p) outliers start: 33 outliers final: 19 residues processed: 121 average time/residue: 0.4412 time to fit residues: 57.2603 Evaluate side-chains 110 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 580 ARG Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 580 ARG Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 108 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 16 optimal weight: 0.0370 chunk 73 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.8664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 107 ASN F 514 ASN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.158767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121251 restraints weight = 7873.361| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.06 r_work: 0.3123 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7689 Z= 0.122 Angle : 0.488 5.000 10488 Z= 0.249 Chirality : 0.043 0.147 1173 Planarity : 0.003 0.025 1329 Dihedral : 3.980 12.867 1197 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.52 % Allowed : 17.30 % Favored : 79.18 % 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: -1.11 (0.26), residues: 957 helix: 0.35 (0.43), residues: 162 sheet: -1.30 (0.33), residues: 240 loop : -0.74 (0.23), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 130 TYR 0.011 0.001 TYR H 105 PHE 0.007 0.001 PHE A 160 TRP 0.009 0.001 TRP I 104 HIS 0.003 0.001 HIS E 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 7674) covalent geometry : angle 0.48464 / 0.25 (10452) SS BOND : bond 0.00097 / 0.06 ( 9) SS BOND : angle 0.18809 / 0.13 ( 18) hydrogen bonds : bond 0.03328 / 2.25 ( 237) hydrogen bonds : angle 4.67197 / 3.43 ( 612) link_BETA1-4 : bond 0.00045 / 0.02 ( 3) link_BETA1-4 : angle 1.84972 / 0.94 ( 9) link_NAG-ASN : bond 0.00121 / 0.06 ( 3) link_NAG-ASN : angle 1.13326 / 0.64 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.191 Fit side-chains REVERT: B 548 MET cc_start: 0.7879 (ptm) cc_final: 0.7598 (ptm) REVERT: B 580 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8292 (mtm-85) REVERT: G 31 ILE cc_start: 0.8071 (mt) cc_final: 0.7832 (mm) REVERT: C 77 THR cc_start: 0.8480 (p) cc_final: 0.7968 (t) REVERT: C 156 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8412 (mt-10) REVERT: D 545 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.6641 (mp0) REVERT: D 580 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8374 (mtm-85) REVERT: H 122 THR cc_start: 0.7893 (p) cc_final: 0.7568 (p) REVERT: F 580 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8114 (mtm-85) REVERT: I 21 SER cc_start: 0.7968 (OUTLIER) cc_final: 0.7405 (t) REVERT: I 122 THR cc_start: 0.7911 (p) cc_final: 0.7650 (p) outliers start: 25 outliers final: 15 residues processed: 105 average time/residue: 0.3611 time to fit residues: 40.9997 Evaluate side-chains 100 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 580 ARG Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 580 ARG Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 580 ARG Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 108 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 24 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.156507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.119231 restraints weight = 8105.525| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.04 r_work: 0.3067 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7689 Z= 0.162 Angle : 0.503 4.999 10488 Z= 0.256 Chirality : 0.043 0.155 1173 Planarity : 0.003 0.025 1329 Dihedral : 3.960 12.446 1197 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.38 % Allowed : 17.58 % Favored : 79.04 % 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: -1.11 (0.25), residues: 957 helix: 0.30 (0.42), residues: 162 sheet: -1.28 (0.33), residues: 240 loop : -0.73 (0.23), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 134 TYR 0.013 0.001 TYR H 105 PHE 0.008 0.001 PHE C 176 TRP 0.006 0.001 TRP I 36 HIS 0.003 0.001 HIS E 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 7674) covalent geometry : angle 0.49885 / 0.26 (10452) SS BOND : bond 0.00145 / 0.10 ( 9) SS BOND : angle 0.24183 / 0.15 ( 18) hydrogen bonds : bond 0.03406 / 2.29 ( 237) hydrogen bonds : angle 4.70073 / 3.45 ( 612) link_BETA1-4 : bond 0.00052 / 0.03 ( 3) link_BETA1-4 : angle 1.98963 / 1.01 ( 9) link_NAG-ASN : bond 0.00036 / 0.02 ( 3) link_NAG-ASN : angle 1.31369 / 0.74 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.284 Fit side-chains REVERT: B 580 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8263 (mtm-85) REVERT: G 31 ILE cc_start: 0.8101 (mt) cc_final: 0.7845 (mm) REVERT: C 156 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8436 (mt-10) REVERT: D 545 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: D 580 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8369 (mtm-85) REVERT: H 122 THR cc_start: 0.7895 (p) cc_final: 0.7569 (p) REVERT: F 580 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8116 (mtm-85) REVERT: I 21 SER cc_start: 0.7974 (OUTLIER) cc_final: 0.7425 (t) REVERT: I 122 THR cc_start: 0.7985 (p) cc_final: 0.7715 (p) outliers start: 24 outliers final: 17 residues processed: 105 average time/residue: 0.3770 time to fit residues: 42.9846 Evaluate side-chains 103 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 580 ARG Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 580 ARG Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 580 ARG Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 108 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.159732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.122444 restraints weight = 7992.757| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.07 r_work: 0.3116 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7689 Z= 0.116 Angle : 0.476 4.944 10488 Z= 0.242 Chirality : 0.042 0.150 1173 Planarity : 0.003 0.025 1329 Dihedral : 3.797 13.126 1197 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.38 % Allowed : 17.86 % Favored : 78.76 % 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: -0.89 (0.26), residues: 957 helix: 0.54 (0.43), residues: 162 sheet: -1.15 (0.34), residues: 234 loop : -0.61 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 130 TYR 0.013 0.001 TYR C 137 PHE 0.006 0.001 PHE C 176 TRP 0.006 0.001 TRP H 104 HIS 0.002 0.001 HIS E 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 7674) covalent geometry : angle 0.47209 / 0.24 (10452) SS BOND : bond 0.00073 / 0.05 ( 9) SS BOND : angle 0.15551 / 0.10 ( 18) hydrogen bonds : bond 0.03102 / 2.10 ( 237) hydrogen bonds : angle 4.49496 / 3.31 ( 612) link_BETA1-4 : bond 0.00099 / 0.05 ( 3) link_BETA1-4 : angle 1.74868 / 0.89 ( 9) link_NAG-ASN : bond 0.00050 / 0.03 ( 3) link_NAG-ASN : angle 1.31831 / 0.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.274 Fit side-chains REVERT: B 520 THR cc_start: 0.7157 (p) cc_final: 0.6691 (p) REVERT: B 580 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8275 (mtm-85) REVERT: G 31 ILE cc_start: 0.8049 (mt) cc_final: 0.7840 (mm) REVERT: C 156 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8394 (mt-10) REVERT: D 580 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8370 (mtm-85) REVERT: H 122 THR cc_start: 0.7849 (p) cc_final: 0.7523 (p) REVERT: F 520 THR cc_start: 0.7152 (p) cc_final: 0.6918 (p) REVERT: F 580 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8128 (mtm-85) REVERT: I 21 SER cc_start: 0.8001 (OUTLIER) cc_final: 0.7428 (t) REVERT: I 122 THR cc_start: 0.7953 (p) cc_final: 0.7684 (p) outliers start: 24 outliers final: 15 residues processed: 104 average time/residue: 0.3275 time to fit residues: 37.1800 Evaluate side-chains 98 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 580 ARG Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 580 ARG Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 580 ARG Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 108 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 0.0270 chunk 30 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 16 optimal weight: 0.0470 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.160858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.123915 restraints weight = 7953.500| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.04 r_work: 0.3154 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7689 Z= 0.093 Angle : 0.456 4.855 10488 Z= 0.233 Chirality : 0.042 0.150 1173 Planarity : 0.003 0.026 1329 Dihedral : 3.629 11.587 1197 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.11 % Allowed : 18.71 % Favored : 79.18 % 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: -0.76 (0.26), residues: 957 helix: 0.78 (0.43), residues: 162 sheet: -1.09 (0.35), residues: 234 loop : -0.55 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 130 TYR 0.009 0.001 TYR A 99 PHE 0.005 0.001 PHE E 160 TRP 0.006 0.001 TRP C 104 HIS 0.003 0.001 HIS B 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.09 ( 7674) covalent geometry : angle 0.45238 / 0.23 (10452) SS BOND : bond 0.00085 / 0.06 ( 9) SS BOND : angle 0.13974 / 0.08 ( 18) hydrogen bonds : bond 0.02892 / 1.96 ( 237) hydrogen bonds : angle 4.35879 / 3.22 ( 612) link_BETA1-4 : bond 0.00144 / 0.07 ( 3) link_BETA1-4 : angle 1.53692 / 0.79 ( 9) link_NAG-ASN : bond 0.00078 / 0.04 ( 3) link_NAG-ASN : angle 1.42313 / 0.78 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.266 Fit side-chains REVERT: B 520 THR cc_start: 0.6932 (p) cc_final: 0.6428 (p) REVERT: B 580 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8288 (mtm-85) REVERT: G 31 ILE cc_start: 0.8036 (mt) cc_final: 0.7823 (mm) REVERT: C 77 THR cc_start: 0.8455 (p) cc_final: 0.7992 (t) REVERT: C 115 LYS cc_start: 0.7552 (mttm) cc_final: 0.7110 (mttp) REVERT: C 156 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8376 (mt-10) REVERT: D 580 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8274 (mtm-85) REVERT: H 122 THR cc_start: 0.7898 (p) cc_final: 0.7565 (p) REVERT: E 59 SER cc_start: 0.8859 (t) cc_final: 0.8644 (p) REVERT: F 580 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8141 (mtm-85) REVERT: I 21 SER cc_start: 0.7985 (OUTLIER) cc_final: 0.7447 (t) REVERT: I 122 THR cc_start: 0.7941 (p) cc_final: 0.7669 (p) outliers start: 15 outliers final: 10 residues processed: 93 average time/residue: 0.3299 time to fit residues: 33.5475 Evaluate side-chains 89 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 580 ARG Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 580 ARG Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 580 ARG Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 108 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 63 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 514 ASN ** B 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.160059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.122941 restraints weight = 7993.258| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.04 r_work: 0.3132 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7689 Z= 0.109 Angle : 0.464 4.872 10488 Z= 0.236 Chirality : 0.042 0.151 1173 Planarity : 0.003 0.025 1329 Dihedral : 3.615 12.198 1197 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.11 % Allowed : 18.99 % Favored : 78.90 % 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: -0.73 (0.26), residues: 957 helix: 0.88 (0.43), residues: 159 sheet: -1.07 (0.35), residues: 234 loop : -0.56 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 164 TYR 0.015 0.001 TYR C 137 PHE 0.006 0.001 PHE C 176 TRP 0.005 0.001 TRP C 104 HIS 0.002 0.001 HIS E 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 7674) covalent geometry : angle 0.46003 / 0.24 (10452) SS BOND : bond 0.00075 / 0.05 ( 9) SS BOND : angle 0.14931 / 0.09 ( 18) hydrogen bonds : bond 0.02962 / 2.01 ( 237) hydrogen bonds : angle 4.30705 / 3.17 ( 612) link_BETA1-4 : bond 0.00114 / 0.06 ( 3) link_BETA1-4 : angle 1.61279 / 0.83 ( 9) link_NAG-ASN : bond 0.00037 / 0.02 ( 3) link_NAG-ASN : angle 1.45785 / 0.80 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2258.03 seconds wall clock time: 39 minutes 11.36 seconds (2351.36 seconds total)