Starting phenix.real_space_refine on Tue Mar 3 12:45:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10xu_75514/03_2026/10xu_75514.cif Found real_map, /net/cci-nas-00/data/ceres_data/10xu_75514/03_2026/10xu_75514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10xu_75514/03_2026/10xu_75514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10xu_75514/03_2026/10xu_75514.map" model { file = "/net/cci-nas-00/data/ceres_data/10xu_75514/03_2026/10xu_75514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10xu_75514/03_2026/10xu_75514.cif" } resolution = 3.18 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= 0.000 sd= 0.001 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: 3 Type Number sf(0) Gaussians C 2760 2.51 5 N 760 2.21 5 O 900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4420 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 442 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Restraints were copied for chains: X, U, C, W, E, B, Y, Z, D Time building chain proxies: 0.57, per 1000 atoms: 0.13 Number of scatterers: 4420 At special positions: 0 Unit cell: (88.51, 96.99, 40.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 900 8.00 N 760 7.00 C 2760 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: 0.36 Conformation dependent library (CDL) restraints added in 185.1 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1080 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 17 sheets defined 0.0% alpha, 34.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 44 through 46 removed outlier: 5.947A pdb=" N LYS A 45 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR A 44 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LYS E 45 " --> pdb=" O GLU D 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 56 removed outlier: 6.455A pdb=" N THR C 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N GLU B 57 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N ALA C 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR B 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N THR A 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N GLU B 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA A 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N THR B 59 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS A 58 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLU B 61 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS A 60 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL B 63 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN A 62 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ASN B 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR A 64 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR A 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N GLU D 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 9.664A pdb=" N ALA A 56 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS D 58 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 63 through 66 removed outlier: 8.416A pdb=" N THR A 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N GLU B 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA A 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N THR B 59 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS A 58 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLU B 61 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS A 60 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL B 63 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN A 62 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ASN B 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR A 64 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR D 64 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A 65 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL D 66 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR E 64 " --> pdb=" O ASN D 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 69 through 71 removed outlier: 6.331A pdb=" N VAL C 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL A 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.424A pdb=" N ALA C 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA A 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 81 through 84 Processing sheet with id=AA7, first strand: chain 'C' and resid 88 through 90 removed outlier: 5.780A pdb=" N ALA A 89 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA D 89 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA E 89 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 95 through 96 removed outlier: 6.033A pdb=" N VAL A 95 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A 96 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL E 95 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'W' and resid 44 through 46 removed outlier: 6.747A pdb=" N THR X 44 " --> pdb=" O LYS U 45 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LYS X 45 " --> pdb=" O GLU Y 46 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS Y 45 " --> pdb=" O GLU Z 46 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'W' and resid 53 through 58 removed outlier: 6.458A pdb=" N THR U 54 " --> pdb=" O VAL W 55 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N GLU W 57 " --> pdb=" O THR U 54 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N ALA U 56 " --> pdb=" O GLU W 57 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR X 54 " --> pdb=" O VAL U 55 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N GLU U 57 " --> pdb=" O THR X 54 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N ALA X 56 " --> pdb=" O GLU U 57 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS Y 58 " --> pdb=" O GLU X 57 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS Z 58 " --> pdb=" O GLU Y 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'W' and resid 63 through 66 Processing sheet with id=AB3, first strand: chain 'W' and resid 69 through 71 removed outlier: 6.380A pdb=" N VAL U 70 " --> pdb=" O VAL W 71 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL X 70 " --> pdb=" O VAL U 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'W' and resid 76 through 78 removed outlier: 6.421A pdb=" N ALA U 76 " --> pdb=" O VAL W 77 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA X 76 " --> pdb=" O VAL U 77 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'W' and resid 84 through 85 removed outlier: 6.089A pdb=" N GLY X 84 " --> pdb=" O ALA Y 85 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLY Y 84 " --> pdb=" O ALA Z 85 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'W' and resid 88 through 90 removed outlier: 6.138A pdb=" N ALA X 89 " --> pdb=" O ALA Y 90 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA Y 89 " --> pdb=" O ALA Z 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'W' and resid 95 through 96 removed outlier: 6.581A pdb=" N VAL X 95 " --> pdb=" O LYS Y 96 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL Y 95 " --> pdb=" O LYS Z 96 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.101A pdb=" N GLY E 84 " --> pdb=" O ALA D 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 65 hydrogen bonds defined for protein. 192 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: 0.43 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 790 1.28 - 1.35: 680 1.35 - 1.42: 180 1.42 - 1.49: 739 1.49 - 1.56: 2051 Bond restraints: 4440 Sorted by residual: bond pdb=" C VAL E 37 " pdb=" O VAL E 37 " ideal model delta sigma weight residual 1.236 1.216 0.019 9.80e-03 1.04e+04 3.93e+00 bond pdb=" C VAL Y 37 " pdb=" O VAL Y 37 " ideal model delta sigma weight residual 1.236 1.217 0.019 9.80e-03 1.04e+04 3.73e+00 bond pdb=" C VAL A 37 " pdb=" O VAL A 37 " ideal model delta sigma weight residual 1.236 1.217 0.019 9.80e-03 1.04e+04 3.62e+00 bond pdb=" C VAL B 37 " pdb=" O VAL B 37 " ideal model delta sigma weight residual 1.236 1.217 0.019 9.80e-03 1.04e+04 3.58e+00 bond pdb=" C VAL Z 37 " pdb=" O VAL Z 37 " ideal model delta sigma weight residual 1.236 1.217 0.018 9.80e-03 1.04e+04 3.50e+00 ... (remaining 4435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 5680 1.30 - 2.61: 220 2.61 - 3.91: 70 3.91 - 5.21: 20 5.21 - 6.52: 10 Bond angle restraints: 6000 Sorted by residual: angle pdb=" CA GLU U 61 " pdb=" CB GLU U 61 " pdb=" CG GLU U 61 " ideal model delta sigma weight residual 114.10 120.62 -6.52 2.00e+00 2.50e-01 1.06e+01 angle pdb=" CA GLU C 61 " pdb=" CB GLU C 61 " pdb=" CG GLU C 61 " ideal model delta sigma weight residual 114.10 120.61 -6.51 2.00e+00 2.50e-01 1.06e+01 angle pdb=" CA GLU W 61 " pdb=" CB GLU W 61 " pdb=" CG GLU W 61 " ideal model delta sigma weight residual 114.10 120.59 -6.49 2.00e+00 2.50e-01 1.05e+01 angle pdb=" CA GLU Y 61 " pdb=" CB GLU Y 61 " pdb=" CG GLU Y 61 " ideal model delta sigma weight residual 114.10 120.59 -6.49 2.00e+00 2.50e-01 1.05e+01 angle pdb=" CA GLU A 61 " pdb=" CB GLU A 61 " pdb=" CG GLU A 61 " ideal model delta sigma weight residual 114.10 120.58 -6.48 2.00e+00 2.50e-01 1.05e+01 ... (remaining 5995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.12: 2030 11.12 - 22.25: 310 22.25 - 33.37: 160 33.37 - 44.49: 50 44.49 - 55.62: 40 Dihedral angle restraints: 2590 sinusoidal: 870 harmonic: 1720 Sorted by residual: dihedral pdb=" CB LYS X 45 " pdb=" CG LYS X 45 " pdb=" CD LYS X 45 " pdb=" CE LYS X 45 " ideal model delta sinusoidal sigma weight residual -60.00 -115.62 55.62 3 1.50e+01 4.44e-03 9.36e+00 dihedral pdb=" CB LYS W 45 " pdb=" CG LYS W 45 " pdb=" CD LYS W 45 " pdb=" CE LYS W 45 " ideal model delta sinusoidal sigma weight residual -60.00 -115.61 55.61 3 1.50e+01 4.44e-03 9.36e+00 dihedral pdb=" CB LYS C 45 " pdb=" CG LYS C 45 " pdb=" CD LYS C 45 " pdb=" CE LYS C 45 " ideal model delta sinusoidal sigma weight residual -60.00 -115.60 55.60 3 1.50e+01 4.44e-03 9.36e+00 ... (remaining 2587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 446 0.038 - 0.075: 134 0.075 - 0.113: 150 0.113 - 0.151: 31 0.151 - 0.188: 19 Chirality restraints: 780 Sorted by residual: chirality pdb=" CB THR W 44 " pdb=" CA THR W 44 " pdb=" OG1 THR W 44 " pdb=" CG2 THR W 44 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.86e-01 chirality pdb=" CB THR C 44 " pdb=" CA THR C 44 " pdb=" OG1 THR C 44 " pdb=" CG2 THR C 44 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.83e-01 chirality pdb=" CB THR A 44 " pdb=" CA THR A 44 " pdb=" OG1 THR A 44 " pdb=" CG2 THR A 44 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.82e-01 ... (remaining 777 not shown) Planarity restraints: 750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL Z 37 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" C VAL Z 37 " -0.023 2.00e-02 2.50e+03 pdb=" O VAL Z 37 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU Z 38 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL Y 37 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C VAL Y 37 " -0.023 2.00e-02 2.50e+03 pdb=" O VAL Y 37 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU Y 38 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 37 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C VAL E 37 " 0.023 2.00e-02 2.50e+03 pdb=" O VAL E 37 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU E 38 " -0.008 2.00e-02 2.50e+03 ... (remaining 747 not shown) Histogram of nonbonded interaction distances: 1.06 - 1.82: 7 1.82 - 2.59: 44 2.59 - 3.36: 4997 3.36 - 4.13: 10781 4.13 - 4.90: 20193 Nonbonded interactions: 36022 Sorted by model distance: nonbonded pdb=" CG2 VAL A 37 " pdb=" OE2 GLU B 35 " model vdw 1.055 3.460 nonbonded pdb=" CG2 VAL X 37 " pdb=" OE2 GLU Y 35 " model vdw 1.436 3.460 nonbonded pdb=" OE2 GLU U 35 " pdb=" CG2 VAL W 37 " model vdw 1.458 3.460 nonbonded pdb=" OE2 GLU C 35 " pdb=" CG2 VAL B 37 " model vdw 1.480 3.460 nonbonded pdb=" CG2 VAL E 37 " pdb=" OE2 GLU D 35 " model vdw 1.485 3.460 ... (remaining 36017 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'X' selection = chain 'U' selection = chain 'C' selection = chain 'W' selection = chain 'E' selection = chain 'B' selection = chain 'Y' selection = chain 'Z' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.300 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 0.036 4440 Z= 0.225 Angle : 0.758 6.517 6000 Z= 0.463 Chirality : 0.063 0.188 780 Planarity : 0.003 0.013 750 Dihedral : 16.843 55.615 1510 Min Nonbonded Distance : 1.055 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.22 % Allowed : 35.56 % Favored : 62.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.28), residues: 620 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.21), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR U 39 PHE 0.008 0.003 PHE E 94 HIS 0.006 0.004 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 4440) covalent geometry : angle 0.75791 ( 6000) hydrogen bonds : bond 0.24274 ( 65) hydrogen bonds : angle 8.54253 ( 192) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.172 Fit side-chains REVERT: X 60 LYS cc_start: 0.7983 (tttt) cc_final: 0.7723 (ttmm) REVERT: X 62 GLN cc_start: 0.7568 (tt0) cc_final: 0.7167 (mt0) REVERT: U 60 LYS cc_start: 0.7766 (tttt) cc_final: 0.7487 (ttmm) REVERT: U 62 GLN cc_start: 0.7475 (tt0) cc_final: 0.7114 (mt0) REVERT: C 60 LYS cc_start: 0.8561 (tttt) cc_final: 0.8216 (ttmm) REVERT: W 57 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: W 60 LYS cc_start: 0.7867 (tttt) cc_final: 0.7502 (ttmm) REVERT: W 62 GLN cc_start: 0.7416 (tt0) cc_final: 0.7160 (mt0) REVERT: E 60 LYS cc_start: 0.7940 (tttt) cc_final: 0.7545 (ttmm) REVERT: E 62 GLN cc_start: 0.7541 (tt0) cc_final: 0.7248 (mt0) REVERT: B 60 LYS cc_start: 0.7649 (tttt) cc_final: 0.7343 (ttmm) REVERT: B 62 GLN cc_start: 0.7339 (tt0) cc_final: 0.7047 (mt0) REVERT: Y 60 LYS cc_start: 0.7922 (tttt) cc_final: 0.7664 (ttmm) REVERT: Y 62 GLN cc_start: 0.7507 (tt0) cc_final: 0.7141 (mt0) REVERT: Z 57 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7101 (pm20) REVERT: Z 60 LYS cc_start: 0.8501 (tttt) cc_final: 0.8210 (ttmm) REVERT: Z 62 GLN cc_start: 0.7913 (tt0) cc_final: 0.7643 (mt0) REVERT: D 60 LYS cc_start: 0.8370 (tttt) cc_final: 0.8039 (ttmm) REVERT: D 62 GLN cc_start: 0.7735 (tt0) cc_final: 0.7413 (mt0) outliers start: 10 outliers final: 0 residues processed: 76 average time/residue: 0.0691 time to fit residues: 6.7435 Evaluate side-chains 68 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain Z residue 57 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.124529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.096868 restraints weight = 5496.829| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.08 r_work: 0.3445 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 4440 Z= 0.337 Angle : 0.618 4.747 6000 Z= 0.349 Chirality : 0.053 0.126 780 Planarity : 0.003 0.010 750 Dihedral : 6.214 31.414 646 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 8.00 % Allowed : 26.89 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.28), residues: 620 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.004 TYR W 39 PHE 0.004 0.002 PHE Y 94 HIS 0.005 0.003 HIS X 50 Details of bonding type rmsd covalent geometry : bond 0.00748 ( 4440) covalent geometry : angle 0.61833 ( 6000) hydrogen bonds : bond 0.03211 ( 65) hydrogen bonds : angle 5.42418 ( 192) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 0.153 Fit side-chains REVERT: A 58 LYS cc_start: 0.7969 (mttt) cc_final: 0.7682 (mtpt) REVERT: A 60 LYS cc_start: 0.8071 (tttt) cc_final: 0.7632 (ttmm) REVERT: X 58 LYS cc_start: 0.8000 (mttt) cc_final: 0.7686 (mtpt) REVERT: U 58 LYS cc_start: 0.8070 (mttt) cc_final: 0.7744 (mtpt) REVERT: C 58 LYS cc_start: 0.8462 (mttt) cc_final: 0.8197 (mtpt) REVERT: C 60 LYS cc_start: 0.8653 (tttt) cc_final: 0.8123 (ttmm) REVERT: W 58 LYS cc_start: 0.8077 (mttt) cc_final: 0.7505 (mmtt) REVERT: W 60 LYS cc_start: 0.8038 (tttt) cc_final: 0.7526 (ttmm) REVERT: E 58 LYS cc_start: 0.7949 (mttt) cc_final: 0.7363 (mmtt) REVERT: E 62 GLN cc_start: 0.7719 (tt0) cc_final: 0.7245 (mt0) REVERT: B 58 LYS cc_start: 0.8219 (mttt) cc_final: 0.7870 (mtpt) REVERT: B 60 LYS cc_start: 0.8076 (tttt) cc_final: 0.7535 (ttmm) REVERT: Y 58 LYS cc_start: 0.7979 (mttt) cc_final: 0.7687 (mtpt) REVERT: Z 58 LYS cc_start: 0.8467 (mttt) cc_final: 0.8181 (mtpt) REVERT: Z 62 GLN cc_start: 0.8118 (tt0) cc_final: 0.7707 (mt0) REVERT: D 58 LYS cc_start: 0.7935 (mttt) cc_final: 0.7626 (mtpt) REVERT: D 60 LYS cc_start: 0.8036 (tttt) cc_final: 0.7511 (ttmm) outliers start: 36 outliers final: 21 residues processed: 133 average time/residue: 0.0824 time to fit residues: 13.5404 Evaluate side-chains 135 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 54 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 58 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 0.0060 chunk 33 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.131539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.102964 restraints weight = 5283.119| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.07 r_work: 0.3532 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4440 Z= 0.099 Angle : 0.442 8.777 6000 Z= 0.239 Chirality : 0.052 0.121 780 Planarity : 0.001 0.007 750 Dihedral : 4.738 15.098 640 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.00 % Allowed : 29.78 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.31), residues: 620 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR X 39 PHE 0.003 0.001 PHE W 94 HIS 0.003 0.001 HIS X 50 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 4440) covalent geometry : angle 0.44193 ( 6000) hydrogen bonds : bond 0.01895 ( 65) hydrogen bonds : angle 4.44459 ( 192) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.169 Fit side-chains REVERT: A 60 LYS cc_start: 0.8027 (tttt) cc_final: 0.7546 (ttmm) REVERT: U 83 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7753 (mp0) REVERT: C 58 LYS cc_start: 0.8361 (mttt) cc_final: 0.8074 (mtpt) REVERT: C 60 LYS cc_start: 0.8605 (tttt) cc_final: 0.8146 (ttmm) REVERT: W 58 LYS cc_start: 0.8009 (mttt) cc_final: 0.7463 (mmtt) REVERT: W 60 LYS cc_start: 0.8009 (tttt) cc_final: 0.7486 (ttmm) REVERT: E 60 LYS cc_start: 0.8154 (tttt) cc_final: 0.7583 (ttmm) REVERT: B 58 LYS cc_start: 0.7984 (mttt) cc_final: 0.7630 (mtpt) REVERT: B 60 LYS cc_start: 0.8046 (tttt) cc_final: 0.7544 (ttmm) REVERT: D 58 LYS cc_start: 0.8010 (mttt) cc_final: 0.7726 (mtpt) REVERT: D 60 LYS cc_start: 0.7960 (tttt) cc_final: 0.7477 (ttmm) outliers start: 9 outliers final: 8 residues processed: 103 average time/residue: 0.0659 time to fit residues: 8.6417 Evaluate side-chains 104 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain Z residue 42 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 46 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.127497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.099627 restraints weight = 5306.463| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.98 r_work: 0.3472 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4440 Z= 0.190 Angle : 0.499 6.728 6000 Z= 0.266 Chirality : 0.051 0.122 780 Planarity : 0.002 0.007 750 Dihedral : 4.988 16.993 640 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.00 % Allowed : 27.56 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.77 (0.31), residues: 620 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR W 39 PHE 0.004 0.001 PHE W 94 HIS 0.004 0.002 HIS X 50 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 4440) covalent geometry : angle 0.49901 ( 6000) hydrogen bonds : bond 0.02229 ( 65) hydrogen bonds : angle 4.70302 ( 192) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.161 Fit side-chains REVERT: A 60 LYS cc_start: 0.8081 (tttt) cc_final: 0.7586 (ttmm) REVERT: U 58 LYS cc_start: 0.8013 (mttt) cc_final: 0.7711 (mtpt) REVERT: U 60 LYS cc_start: 0.8024 (tttt) cc_final: 0.7592 (ttmm) REVERT: U 83 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7836 (mp0) REVERT: C 58 LYS cc_start: 0.8456 (mttt) cc_final: 0.8181 (mtpt) REVERT: C 60 LYS cc_start: 0.8630 (tttt) cc_final: 0.8152 (ttmm) REVERT: W 58 LYS cc_start: 0.8048 (mttt) cc_final: 0.7464 (mmtt) REVERT: W 60 LYS cc_start: 0.8020 (tttt) cc_final: 0.7503 (ttmm) REVERT: E 60 LYS cc_start: 0.8195 (tttt) cc_final: 0.7604 (ttmm) REVERT: B 58 LYS cc_start: 0.8081 (mttt) cc_final: 0.7717 (mtpt) REVERT: B 60 LYS cc_start: 0.8103 (tttt) cc_final: 0.7592 (ttmm) REVERT: Z 58 LYS cc_start: 0.8437 (mttt) cc_final: 0.8143 (mtpt) REVERT: D 58 LYS cc_start: 0.7996 (mttt) cc_final: 0.7707 (mtpt) REVERT: D 60 LYS cc_start: 0.7991 (tttt) cc_final: 0.7505 (ttmm) outliers start: 18 outliers final: 18 residues processed: 116 average time/residue: 0.0780 time to fit residues: 11.1762 Evaluate side-chains 124 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain D residue 42 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 40 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.128166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.100187 restraints weight = 5296.858| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.98 r_work: 0.3489 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4440 Z= 0.158 Angle : 0.529 9.152 6000 Z= 0.261 Chirality : 0.051 0.121 780 Planarity : 0.002 0.007 750 Dihedral : 4.840 16.774 640 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.22 % Allowed : 27.78 % Favored : 68.00 % 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: -1.65 (0.32), residues: 620 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR Z 39 PHE 0.004 0.001 PHE W 94 HIS 0.004 0.002 HIS X 50 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 4440) covalent geometry : angle 0.52912 ( 6000) hydrogen bonds : bond 0.01961 ( 65) hydrogen bonds : angle 4.59316 ( 192) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.161 Fit side-chains REVERT: A 60 LYS cc_start: 0.8061 (tttt) cc_final: 0.7554 (ttmm) REVERT: U 58 LYS cc_start: 0.7973 (mttt) cc_final: 0.7667 (mtpt) REVERT: U 60 LYS cc_start: 0.8054 (tttt) cc_final: 0.7582 (ttmm) REVERT: U 83 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7845 (mp0) REVERT: C 58 LYS cc_start: 0.8428 (mttt) cc_final: 0.8153 (mtpt) REVERT: C 60 LYS cc_start: 0.8641 (tttt) cc_final: 0.8152 (ttmm) REVERT: W 58 LYS cc_start: 0.8050 (mttt) cc_final: 0.7444 (mmtt) REVERT: W 60 LYS cc_start: 0.8003 (tttt) cc_final: 0.7468 (ttmm) REVERT: E 60 LYS cc_start: 0.8182 (tttt) cc_final: 0.7586 (ttmm) REVERT: B 58 LYS cc_start: 0.8044 (mttt) cc_final: 0.7715 (mtpt) REVERT: B 60 LYS cc_start: 0.8083 (tttt) cc_final: 0.7564 (ttmm) REVERT: Z 58 LYS cc_start: 0.8447 (mttt) cc_final: 0.8144 (mtpt) REVERT: D 58 LYS cc_start: 0.7980 (mttt) cc_final: 0.7685 (mtpt) REVERT: D 60 LYS cc_start: 0.8004 (tttt) cc_final: 0.7505 (ttmm) outliers start: 19 outliers final: 17 residues processed: 119 average time/residue: 0.0737 time to fit residues: 10.7912 Evaluate side-chains 121 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain D residue 42 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 24 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 59 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.128700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.100576 restraints weight = 5384.595| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 3.01 r_work: 0.3490 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4440 Z= 0.151 Angle : 0.529 8.708 6000 Z= 0.261 Chirality : 0.051 0.121 780 Planarity : 0.002 0.009 750 Dihedral : 4.765 16.753 640 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 5.11 % Allowed : 26.00 % Favored : 68.89 % 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: -1.58 (0.33), residues: 620 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR U 39 PHE 0.004 0.001 PHE W 94 HIS 0.004 0.002 HIS X 50 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 4440) covalent geometry : angle 0.52885 ( 6000) hydrogen bonds : bond 0.01874 ( 65) hydrogen bonds : angle 4.56926 ( 192) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.173 Fit side-chains REVERT: A 60 LYS cc_start: 0.8070 (tttt) cc_final: 0.7634 (ttmm) REVERT: U 58 LYS cc_start: 0.7982 (mttt) cc_final: 0.7681 (mtpt) REVERT: U 60 LYS cc_start: 0.8064 (tttt) cc_final: 0.7567 (ttmm) REVERT: C 58 LYS cc_start: 0.8441 (mttt) cc_final: 0.8159 (mtpt) REVERT: C 60 LYS cc_start: 0.8634 (tttt) cc_final: 0.8152 (ttmm) REVERT: W 58 LYS cc_start: 0.8053 (mttt) cc_final: 0.7450 (mmtt) REVERT: W 60 LYS cc_start: 0.8010 (tttt) cc_final: 0.7413 (ttmm) REVERT: E 60 LYS cc_start: 0.8202 (tttt) cc_final: 0.7586 (ttmm) REVERT: B 58 LYS cc_start: 0.8059 (mttt) cc_final: 0.7725 (mtpt) REVERT: B 60 LYS cc_start: 0.8095 (tttt) cc_final: 0.7573 (ttmm) REVERT: Z 58 LYS cc_start: 0.8432 (mttt) cc_final: 0.8131 (mtpt) REVERT: D 58 LYS cc_start: 0.7999 (mttt) cc_final: 0.7740 (mtpt) REVERT: D 60 LYS cc_start: 0.8013 (tttt) cc_final: 0.7525 (ttmm) outliers start: 23 outliers final: 20 residues processed: 124 average time/residue: 0.0774 time to fit residues: 11.9056 Evaluate side-chains 127 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 54 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.127908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.099794 restraints weight = 5320.780| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.99 r_work: 0.3484 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4440 Z= 0.156 Angle : 0.542 9.155 6000 Z= 0.268 Chirality : 0.051 0.121 780 Planarity : 0.002 0.010 750 Dihedral : 4.767 16.972 640 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.44 % Allowed : 25.11 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.54 (0.33), residues: 620 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR U 39 PHE 0.003 0.001 PHE W 94 HIS 0.004 0.002 HIS X 50 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 4440) covalent geometry : angle 0.54248 ( 6000) hydrogen bonds : bond 0.01868 ( 65) hydrogen bonds : angle 4.60195 ( 192) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.165 Fit side-chains REVERT: A 60 LYS cc_start: 0.8189 (tttt) cc_final: 0.7618 (ttmm) REVERT: U 58 LYS cc_start: 0.7952 (mttt) cc_final: 0.7642 (mtpt) REVERT: U 60 LYS cc_start: 0.8010 (tttt) cc_final: 0.7572 (ttmm) REVERT: U 83 GLU cc_start: 0.7964 (mp0) cc_final: 0.7669 (mp0) REVERT: C 58 LYS cc_start: 0.8428 (mttt) cc_final: 0.8152 (mtpt) REVERT: C 60 LYS cc_start: 0.8641 (tttt) cc_final: 0.8147 (ttmm) REVERT: W 58 LYS cc_start: 0.8057 (mttt) cc_final: 0.7490 (mmtt) REVERT: W 60 LYS cc_start: 0.7980 (tttt) cc_final: 0.7405 (ttmm) REVERT: E 60 LYS cc_start: 0.8170 (tttt) cc_final: 0.7570 (ttmm) REVERT: B 58 LYS cc_start: 0.8033 (mttt) cc_final: 0.7704 (mtpt) REVERT: B 60 LYS cc_start: 0.8113 (tttt) cc_final: 0.7585 (ttmm) REVERT: Y 83 GLU cc_start: 0.8130 (mp0) cc_final: 0.7864 (mp0) REVERT: Z 58 LYS cc_start: 0.8459 (mttt) cc_final: 0.8150 (mtpt) REVERT: D 58 LYS cc_start: 0.8001 (mttt) cc_final: 0.7694 (mtpt) REVERT: D 60 LYS cc_start: 0.8061 (tttt) cc_final: 0.7517 (ttmm) outliers start: 20 outliers final: 18 residues processed: 122 average time/residue: 0.0743 time to fit residues: 11.3514 Evaluate side-chains 126 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 54 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.124621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.096300 restraints weight = 5500.423| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.05 r_work: 0.3459 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 4440 Z= 0.258 Angle : 0.603 9.157 6000 Z= 0.303 Chirality : 0.052 0.123 780 Planarity : 0.002 0.012 750 Dihedral : 5.191 17.727 640 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.89 % Allowed : 24.89 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.32), residues: 620 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR U 39 PHE 0.004 0.001 PHE E 94 HIS 0.004 0.002 HIS X 50 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 4440) covalent geometry : angle 0.60330 ( 6000) hydrogen bonds : bond 0.02329 ( 65) hydrogen bonds : angle 4.91519 ( 192) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.142 Fit side-chains REVERT: A 60 LYS cc_start: 0.8203 (tttt) cc_final: 0.7686 (ttmm) REVERT: X 60 LYS cc_start: 0.8155 (tttt) cc_final: 0.7636 (ttmm) REVERT: U 58 LYS cc_start: 0.8025 (mttt) cc_final: 0.7735 (mtpt) REVERT: C 58 LYS cc_start: 0.8454 (mttt) cc_final: 0.8132 (mtmm) REVERT: C 60 LYS cc_start: 0.8666 (tttt) cc_final: 0.8173 (ttmm) REVERT: W 58 LYS cc_start: 0.8116 (mttt) cc_final: 0.7526 (mmtt) REVERT: W 60 LYS cc_start: 0.8074 (tttt) cc_final: 0.7526 (ttmm) REVERT: E 60 LYS cc_start: 0.8272 (tttt) cc_final: 0.7673 (ttmm) REVERT: B 58 LYS cc_start: 0.8121 (mttt) cc_final: 0.7813 (mtpt) REVERT: B 60 LYS cc_start: 0.8228 (tttt) cc_final: 0.7638 (ttmm) REVERT: Y 83 GLU cc_start: 0.8194 (mp0) cc_final: 0.7940 (mp0) REVERT: Z 58 LYS cc_start: 0.8496 (mttt) cc_final: 0.8195 (mtpt) REVERT: D 58 LYS cc_start: 0.8062 (mttt) cc_final: 0.7754 (mtpt) REVERT: D 60 LYS cc_start: 0.8130 (tttt) cc_final: 0.7623 (ttmm) outliers start: 22 outliers final: 21 residues processed: 133 average time/residue: 0.0777 time to fit residues: 12.7422 Evaluate side-chains 141 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 54 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 15 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.130877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.102438 restraints weight = 5321.304| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 3.01 r_work: 0.3531 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4440 Z= 0.101 Angle : 0.560 9.436 6000 Z= 0.267 Chirality : 0.051 0.122 780 Planarity : 0.002 0.013 750 Dihedral : 4.542 16.733 640 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.22 % Allowed : 28.00 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.51 (0.33), residues: 620 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR U 39 PHE 0.003 0.001 PHE W 94 HIS 0.004 0.002 HIS X 50 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 4440) covalent geometry : angle 0.55954 ( 6000) hydrogen bonds : bond 0.01501 ( 65) hydrogen bonds : angle 4.44251 ( 192) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.172 Fit side-chains REVERT: A 60 LYS cc_start: 0.8165 (tttt) cc_final: 0.7629 (ttmm) REVERT: U 58 LYS cc_start: 0.7998 (mttt) cc_final: 0.7700 (mtpt) REVERT: U 60 LYS cc_start: 0.7774 (tttt) cc_final: 0.7412 (ttmm) REVERT: U 83 GLU cc_start: 0.8245 (mp0) cc_final: 0.7824 (mp0) REVERT: C 60 LYS cc_start: 0.8653 (tttt) cc_final: 0.8157 (ttmm) REVERT: W 58 LYS cc_start: 0.8110 (mttt) cc_final: 0.7506 (mmtt) REVERT: W 60 LYS cc_start: 0.7986 (tttt) cc_final: 0.7430 (ttmm) REVERT: E 60 LYS cc_start: 0.8194 (tttt) cc_final: 0.7583 (ttmm) REVERT: B 60 LYS cc_start: 0.8114 (tttt) cc_final: 0.7586 (ttmm) REVERT: Y 83 GLU cc_start: 0.8127 (mp0) cc_final: 0.7862 (mp0) REVERT: Z 58 LYS cc_start: 0.8400 (mttt) cc_final: 0.8085 (mtpt) REVERT: D 58 LYS cc_start: 0.7973 (mttt) cc_final: 0.7666 (mtpt) REVERT: D 60 LYS cc_start: 0.8077 (tttt) cc_final: 0.7556 (ttmm) outliers start: 10 outliers final: 10 residues processed: 112 average time/residue: 0.0744 time to fit residues: 10.3732 Evaluate side-chains 113 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain Y residue 42 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.125362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.097155 restraints weight = 5429.786| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.99 r_work: 0.3451 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4440 Z= 0.236 Angle : 0.610 9.455 6000 Z= 0.302 Chirality : 0.052 0.120 780 Planarity : 0.002 0.013 750 Dihedral : 5.087 18.137 640 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.67 % Allowed : 27.78 % Favored : 69.56 % 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: -1.63 (0.32), residues: 620 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR U 39 PHE 0.003 0.001 PHE E 94 HIS 0.004 0.002 HIS X 50 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 4440) covalent geometry : angle 0.61006 ( 6000) hydrogen bonds : bond 0.02223 ( 65) hydrogen bonds : angle 4.85279 ( 192) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.131 Fit side-chains REVERT: A 60 LYS cc_start: 0.8202 (tttt) cc_final: 0.7662 (ttmm) REVERT: U 58 LYS cc_start: 0.8009 (mttt) cc_final: 0.7718 (mtpt) REVERT: C 58 LYS cc_start: 0.8466 (mttt) cc_final: 0.8125 (mtmm) REVERT: C 60 LYS cc_start: 0.8730 (tttt) cc_final: 0.8201 (ttmm) REVERT: W 58 LYS cc_start: 0.8109 (mttt) cc_final: 0.7485 (mmtt) REVERT: W 60 LYS cc_start: 0.8105 (tttt) cc_final: 0.7544 (ttmm) REVERT: E 60 LYS cc_start: 0.8284 (tttt) cc_final: 0.7671 (ttmm) REVERT: B 58 LYS cc_start: 0.8075 (mttt) cc_final: 0.7758 (mtpt) REVERT: B 60 LYS cc_start: 0.8239 (tttt) cc_final: 0.7631 (ttmm) REVERT: Z 58 LYS cc_start: 0.8537 (mttt) cc_final: 0.8218 (mtpt) REVERT: D 58 LYS cc_start: 0.8038 (mttt) cc_final: 0.7717 (mtpt) REVERT: D 60 LYS cc_start: 0.8142 (tttt) cc_final: 0.7632 (ttmm) outliers start: 12 outliers final: 12 residues processed: 123 average time/residue: 0.0736 time to fit residues: 11.3268 Evaluate side-chains 127 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain Y residue 42 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.127414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.099093 restraints weight = 5385.406| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.00 r_work: 0.3480 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4440 Z= 0.163 Angle : 0.623 9.620 6000 Z= 0.301 Chirality : 0.051 0.121 780 Planarity : 0.002 0.013 750 Dihedral : 4.857 18.029 640 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.89 % Allowed : 28.89 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.32), residues: 620 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR U 39 PHE 0.003 0.001 PHE W 94 HIS 0.004 0.002 HIS X 50 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 4440) covalent geometry : angle 0.62313 ( 6000) hydrogen bonds : bond 0.01871 ( 65) hydrogen bonds : angle 4.69967 ( 192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1207.59 seconds wall clock time: 21 minutes 20.45 seconds (1280.45 seconds total)