Starting phenix.real_space_refine on Tue Feb 3 13:16:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ji8_61500/02_2026/9ji8_61500.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ji8_61500/02_2026/9ji8_61500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ji8_61500/02_2026/9ji8_61500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ji8_61500/02_2026/9ji8_61500.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ji8_61500/02_2026/9ji8_61500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ji8_61500/02_2026/9ji8_61500.map" } resolution = 2.85 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= 0.002 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 1896 2.51 5 N 528 2.21 5 O 606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3030 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 67 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "F" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Restraints were copied for chains: H, E, I, J, N, K, G, L, M, O Time building chain proxies: 0.51, per 1000 atoms: 0.17 Number of scatterers: 3030 At special positions: 0 Unit cell: (94.62, 118.69, 30.71, 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 606 8.00 N 528 7.00 C 1896 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: 0.23 Conformation dependent library (CDL) restraints added in 126.9 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 37.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'F' and resid 46 through 56 removed outlier: 7.472A pdb=" N GLY F 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N HIS G 50 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N VAL F 49 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N VAL G 52 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY F 51 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N THR G 54 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA F 53 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ALA G 56 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL F 55 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY G 47 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N HIS M 50 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N VAL G 49 " --> pdb=" O HIS M 50 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N VAL M 52 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLY G 51 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N THR M 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA G 53 " --> pdb=" O THR M 54 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N ALA M 56 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL G 55 " --> pdb=" O ALA M 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 60 through 66 Processing sheet with id=AA3, first strand: chain 'F' and resid 69 through 72 Processing sheet with id=AA4, first strand: chain 'F' and resid 75 through 82 removed outlier: 6.080A pdb=" N THR F 75 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ALA G 78 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL F 77 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N LYS G 80 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLN F 79 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N VAL G 82 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR F 81 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR G 75 " --> pdb=" O ALA M 76 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ALA M 78 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL G 77 " --> pdb=" O ALA M 78 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N LYS M 80 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN G 79 " --> pdb=" O LYS M 80 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N VAL M 82 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR G 81 " --> pdb=" O VAL M 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 91 through 92 removed outlier: 6.517A pdb=" N ALA F 91 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA G 91 " --> pdb=" O THR M 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'K' and resid 46 through 56 removed outlier: 7.555A pdb=" N GLY K 47 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N HIS L 50 " --> pdb=" O GLY K 47 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N VAL K 49 " --> pdb=" O HIS L 50 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N VAL L 52 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY K 51 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N THR L 54 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA K 53 " --> pdb=" O THR L 54 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N ALA L 56 " --> pdb=" O ALA K 53 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL K 55 " --> pdb=" O ALA L 56 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLY L 47 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 10.073A pdb=" N HIS O 50 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N VAL L 49 " --> pdb=" O HIS O 50 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N VAL O 52 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY L 51 " --> pdb=" O VAL O 52 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N THR O 54 " --> pdb=" O GLY L 51 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA L 53 " --> pdb=" O THR O 54 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ALA O 56 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL L 55 " --> pdb=" O ALA O 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'K' and resid 60 through 66 removed outlier: 6.278A pdb=" N LYS K 60 " --> pdb=" O GLU L 61 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N VAL L 63 " --> pdb=" O LYS K 60 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLN K 62 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ASN L 65 " --> pdb=" O GLN K 62 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N THR K 64 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 69 through 72 Processing sheet with id=AA9, first strand: chain 'K' and resid 75 through 82 removed outlier: 6.068A pdb=" N THR K 75 " --> pdb=" O ALA L 76 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ALA L 78 " --> pdb=" O THR K 75 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL K 77 " --> pdb=" O ALA L 78 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N LYS L 80 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLN K 79 " --> pdb=" O LYS L 80 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL L 82 " --> pdb=" O GLN K 79 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR K 81 " --> pdb=" O VAL L 82 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N THR L 75 " --> pdb=" O ALA O 76 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ALA O 78 " --> pdb=" O THR L 75 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL L 77 " --> pdb=" O ALA O 78 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N LYS O 80 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLN L 79 " --> pdb=" O LYS O 80 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N VAL O 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR L 81 " --> pdb=" O VAL O 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 91 through 92 removed outlier: 6.402A pdb=" N ALA K 91 " --> pdb=" O THR L 92 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA L 91 " --> pdb=" O THR O 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 30 hydrogen bonds defined for protein. 90 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: 0.32 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 534 1.29 - 1.35: 462 1.35 - 1.41: 101 1.41 - 1.48: 511 1.48 - 1.54: 1428 Bond restraints: 3036 Sorted by residual: bond pdb=" CA LYS G 96 " pdb=" CB LYS G 96 " ideal model delta sigma weight residual 1.531 1.483 0.048 3.28e-02 9.30e+02 2.10e+00 bond pdb=" CA LYS L 96 " pdb=" CB LYS L 96 " ideal model delta sigma weight residual 1.531 1.483 0.047 3.28e-02 9.30e+02 2.10e+00 bond pdb=" CA LYS K 96 " pdb=" CB LYS K 96 " ideal model delta sigma weight residual 1.531 1.483 0.047 3.28e-02 9.30e+02 2.08e+00 bond pdb=" CA LYS M 96 " pdb=" CB LYS M 96 " ideal model delta sigma weight residual 1.531 1.484 0.047 3.28e-02 9.30e+02 2.07e+00 bond pdb=" CA LYS F 96 " pdb=" CB LYS F 96 " ideal model delta sigma weight residual 1.531 1.484 0.047 3.28e-02 9.30e+02 2.07e+00 ... (remaining 3031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.81: 3409 0.81 - 1.61: 478 1.61 - 2.42: 151 2.42 - 3.23: 30 3.23 - 4.03: 24 Bond angle restraints: 4092 Sorted by residual: angle pdb=" C ILE K 88 " pdb=" N ALA K 89 " pdb=" CA ALA K 89 " ideal model delta sigma weight residual 123.34 119.31 4.03 1.80e+00 3.09e-01 5.02e+00 angle pdb=" C ILE G 88 " pdb=" N ALA G 89 " pdb=" CA ALA G 89 " ideal model delta sigma weight residual 123.34 119.32 4.02 1.80e+00 3.09e-01 4.98e+00 angle pdb=" C ILE O 88 " pdb=" N ALA O 89 " pdb=" CA ALA O 89 " ideal model delta sigma weight residual 123.34 119.33 4.01 1.80e+00 3.09e-01 4.96e+00 angle pdb=" C ILE L 88 " pdb=" N ALA L 89 " pdb=" CA ALA L 89 " ideal model delta sigma weight residual 123.34 119.36 3.98 1.80e+00 3.09e-01 4.89e+00 angle pdb=" C ILE F 88 " pdb=" N ALA F 89 " pdb=" CA ALA F 89 " ideal model delta sigma weight residual 123.34 119.36 3.98 1.80e+00 3.09e-01 4.89e+00 ... (remaining 4087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.50: 1554 11.50 - 23.00: 150 23.00 - 34.50: 54 34.50 - 46.00: 12 46.00 - 57.49: 24 Dihedral angle restraints: 1794 sinusoidal: 606 harmonic: 1188 Sorted by residual: dihedral pdb=" CA ASP O 98 " pdb=" CB ASP O 98 " pdb=" CG ASP O 98 " pdb=" OD1 ASP O 98 " ideal model delta sinusoidal sigma weight residual -30.00 -83.14 53.14 1 2.00e+01 2.50e-03 9.60e+00 dihedral pdb=" CA ASP L 98 " pdb=" CB ASP L 98 " pdb=" CG ASP L 98 " pdb=" OD1 ASP L 98 " ideal model delta sinusoidal sigma weight residual -30.00 -83.13 53.13 1 2.00e+01 2.50e-03 9.60e+00 dihedral pdb=" CA ASP K 98 " pdb=" CB ASP K 98 " pdb=" CG ASP K 98 " pdb=" OD1 ASP K 98 " ideal model delta sinusoidal sigma weight residual -30.00 -83.13 53.13 1 2.00e+01 2.50e-03 9.60e+00 ... (remaining 1791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 216 0.029 - 0.057: 146 0.057 - 0.086: 83 0.086 - 0.115: 65 0.115 - 0.143: 30 Chirality restraints: 540 Sorted by residual: chirality pdb=" CB THR G 72 " pdb=" CA THR G 72 " pdb=" OG1 THR G 72 " pdb=" CG2 THR G 72 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CB THR K 72 " pdb=" CA THR K 72 " pdb=" OG1 THR K 72 " pdb=" CG2 THR K 72 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CB THR M 72 " pdb=" CA THR M 72 " pdb=" OG1 THR M 72 " pdb=" CG2 THR M 72 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 537 not shown) Planarity restraints: 504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS K 50 " 0.012 2.00e-02 2.50e+03 1.04e-02 1.64e+00 pdb=" CG HIS K 50 " -0.022 2.00e-02 2.50e+03 pdb=" ND1 HIS K 50 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS K 50 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS K 50 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS K 50 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 50 " 0.012 2.00e-02 2.50e+03 1.04e-02 1.62e+00 pdb=" CG HIS G 50 " -0.022 2.00e-02 2.50e+03 pdb=" ND1 HIS G 50 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS G 50 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS G 50 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS G 50 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS L 50 " 0.012 2.00e-02 2.50e+03 1.01e-02 1.53e+00 pdb=" CG HIS L 50 " -0.021 2.00e-02 2.50e+03 pdb=" ND1 HIS L 50 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS L 50 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS L 50 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS L 50 " 0.003 2.00e-02 2.50e+03 ... (remaining 501 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 88 2.70 - 3.25: 2775 3.25 - 3.80: 4456 3.80 - 4.35: 5463 4.35 - 4.90: 11108 Nonbonded interactions: 23890 Sorted by model distance: nonbonded pdb=" OE1 GLN M 79 " pdb=" OG1 THR M 81 " model vdw 2.148 3.040 nonbonded pdb=" OE1 GLN F 79 " pdb=" OG1 THR F 81 " model vdw 2.148 3.040 nonbonded pdb=" OE1 GLN L 79 " pdb=" OG1 THR L 81 " model vdw 2.148 3.040 nonbonded pdb=" OE1 GLN O 79 " pdb=" OG1 THR O 81 " model vdw 2.148 3.040 nonbonded pdb=" OE1 GLN K 79 " pdb=" OG1 THR K 81 " model vdw 2.149 3.040 ... (remaining 23885 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 'D' selection = chain 'H' selection = chain 'E' selection = chain 'I' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'G' selection = chain 'L' selection = chain 'M' selection = chain 'O' } 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: 3.120 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.700 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 : 0.008 0.048 3036 Z= 0.371 Angle : 0.730 4.033 4092 Z= 0.421 Chirality : 0.060 0.143 540 Planarity : 0.003 0.010 504 Dihedral : 13.582 57.493 1038 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.34), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR L 39 PHE 0.014 0.004 PHE F 94 HIS 0.009 0.005 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00845 ( 3036) covalent geometry : angle 0.73045 ( 4092) hydrogen bonds : bond 0.12125 ( 30) hydrogen bonds : angle 5.94376 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.111 Fit side-chains REVERT: K 60 LYS cc_start: 0.7715 (tttt) cc_final: 0.7515 (tttp) REVERT: G 60 LYS cc_start: 0.7764 (tttt) cc_final: 0.7494 (tttp) REVERT: L 60 LYS cc_start: 0.7766 (tttt) cc_final: 0.7495 (tttm) REVERT: M 60 LYS cc_start: 0.7980 (tttt) cc_final: 0.7549 (tttm) REVERT: O 80 LYS cc_start: 0.8404 (tttm) cc_final: 0.8052 (tttt) REVERT: O 96 LYS cc_start: 0.7525 (tttt) cc_final: 0.7199 (ttmt) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.6290 time to fit residues: 28.3283 Evaluate side-chains 40 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 HIS F 65 ASN F 79 GLN K 50 HIS K 65 ASN G 50 HIS G 65 ASN G 79 GLN L 50 HIS L 65 ASN L 79 GLN M 50 HIS M 65 ASN M 79 GLN O 50 HIS O 65 ASN O 79 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.184876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.144244 restraints weight = 3027.306| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 2.19 r_work: 0.4162 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.4023 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3036 Z= 0.107 Angle : 0.455 3.179 4092 Z= 0.258 Chirality : 0.052 0.139 540 Planarity : 0.001 0.009 504 Dihedral : 4.279 13.115 432 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.61 % Allowed : 13.07 % Favored : 84.31 % 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: -2.82 (0.38), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR K 39 PHE 0.010 0.002 PHE O 94 HIS 0.004 0.002 HIS O 50 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 3036) covalent geometry : angle 0.45486 ( 4092) hydrogen bonds : bond 0.02223 ( 30) hydrogen bonds : angle 4.72683 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.070 Fit side-chains REVERT: K 60 LYS cc_start: 0.7852 (tttt) cc_final: 0.7575 (tttm) REVERT: G 60 LYS cc_start: 0.7835 (tttt) cc_final: 0.7484 (tttp) REVERT: L 60 LYS cc_start: 0.7787 (tttt) cc_final: 0.7453 (tttm) REVERT: M 43 LYS cc_start: 0.8281 (mtpm) cc_final: 0.8060 (mtpt) REVERT: M 60 LYS cc_start: 0.8205 (tttt) cc_final: 0.7743 (tttm) outliers start: 8 outliers final: 4 residues processed: 48 average time/residue: 0.5759 time to fit residues: 28.3175 Evaluate side-chains 39 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain L residue 37 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 35 optimal weight: 30.0000 chunk 25 optimal weight: 7.9990 chunk 38 optimal weight: 0.1980 chunk 28 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 8 optimal weight: 0.0010 chunk 7 optimal weight: 20.0000 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.181076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.139432 restraints weight = 3009.275| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 2.21 r_work: 0.4106 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3966 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3036 Z= 0.129 Angle : 0.476 3.389 4092 Z= 0.270 Chirality : 0.051 0.136 540 Planarity : 0.002 0.006 504 Dihedral : 4.310 12.215 432 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.92 % Allowed : 15.36 % Favored : 80.72 % 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: -2.54 (0.40), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR M 39 PHE 0.011 0.003 PHE G 94 HIS 0.004 0.002 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3036) covalent geometry : angle 0.47644 ( 4092) hydrogen bonds : bond 0.02205 ( 30) hydrogen bonds : angle 4.30972 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.127 Fit side-chains REVERT: K 60 LYS cc_start: 0.7893 (tttt) cc_final: 0.7625 (tttm) REVERT: G 60 LYS cc_start: 0.7805 (tttt) cc_final: 0.7468 (tttp) REVERT: L 60 LYS cc_start: 0.7804 (tttt) cc_final: 0.7448 (tttm) REVERT: M 43 LYS cc_start: 0.8279 (mtpm) cc_final: 0.8057 (mtpt) REVERT: M 60 LYS cc_start: 0.8201 (tttt) cc_final: 0.7735 (tttm) outliers start: 12 outliers final: 5 residues processed: 50 average time/residue: 0.4434 time to fit residues: 22.8834 Evaluate side-chains 38 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain O residue 37 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 30.0000 chunk 3 optimal weight: 10.0000 chunk 1 optimal weight: 0.1980 chunk 21 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 overall best weight: 6.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 GLN K 79 GLN G 79 GLN L 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.170029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.127322 restraints weight = 3102.157| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 2.28 r_work: 0.3969 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3827 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.039 3036 Z= 0.445 Angle : 0.789 5.674 4092 Z= 0.453 Chirality : 0.062 0.146 540 Planarity : 0.003 0.009 504 Dihedral : 5.395 14.329 432 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.56 % Favored : 87.44 % Rotamer: Outliers : 7.19 % Allowed : 12.09 % Favored : 80.72 % 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: -2.49 (0.40), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR M 39 PHE 0.020 0.005 PHE G 94 HIS 0.006 0.004 HIS M 50 Details of bonding type rmsd covalent geometry : bond 0.00979 ( 3036) covalent geometry : angle 0.78852 ( 4092) hydrogen bonds : bond 0.03071 ( 30) hydrogen bonds : angle 4.45496 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 44 time to evaluate : 0.141 Fit side-chains REVERT: F 96 LYS cc_start: 0.7049 (tttt) cc_final: 0.6622 (tttm) REVERT: K 60 LYS cc_start: 0.7889 (tttt) cc_final: 0.7574 (tttm) REVERT: G 60 LYS cc_start: 0.7827 (tttt) cc_final: 0.7481 (tttm) REVERT: G 96 LYS cc_start: 0.7110 (tttt) cc_final: 0.6834 (tttp) REVERT: L 60 LYS cc_start: 0.7811 (tttt) cc_final: 0.7433 (tttm) REVERT: M 60 LYS cc_start: 0.8289 (tttt) cc_final: 0.7809 (tttp) REVERT: O 96 LYS cc_start: 0.7566 (tttt) cc_final: 0.7082 (ttmt) outliers start: 22 outliers final: 11 residues processed: 64 average time/residue: 0.4072 time to fit residues: 26.9874 Evaluate side-chains 55 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 60 LYS Chi-restraints excluded: chain O residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.178224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.136752 restraints weight = 3009.527| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 2.25 r_work: 0.4082 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3942 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3036 Z= 0.143 Angle : 0.489 3.632 4092 Z= 0.276 Chirality : 0.053 0.139 540 Planarity : 0.002 0.006 504 Dihedral : 4.540 12.582 432 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 4.90 % Allowed : 17.32 % Favored : 77.78 % 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: -2.20 (0.41), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR L 39 PHE 0.011 0.003 PHE G 94 HIS 0.005 0.003 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 3036) covalent geometry : angle 0.48932 ( 4092) hydrogen bonds : bond 0.02063 ( 30) hydrogen bonds : angle 4.28735 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 33 time to evaluate : 0.111 Fit side-chains REVERT: K 60 LYS cc_start: 0.7889 (tttt) cc_final: 0.7598 (tttm) REVERT: G 60 LYS cc_start: 0.7790 (tttt) cc_final: 0.7467 (tttm) REVERT: L 60 LYS cc_start: 0.7723 (tttt) cc_final: 0.7345 (tttm) REVERT: M 43 LYS cc_start: 0.8362 (mtpm) cc_final: 0.7897 (mttp) REVERT: M 60 LYS cc_start: 0.8196 (tttt) cc_final: 0.7727 (tttm) outliers start: 15 outliers final: 10 residues processed: 47 average time/residue: 0.4611 time to fit residues: 22.4147 Evaluate side-chains 43 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 41 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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 = 0.4616 r_free = 0.4616 target = 0.176841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.138562 restraints weight = 3209.734| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 2.14 r_work: 0.4073 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3933 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3036 Z= 0.171 Angle : 0.504 3.775 4092 Z= 0.287 Chirality : 0.052 0.137 540 Planarity : 0.002 0.006 504 Dihedral : 4.555 12.664 432 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.92 % Allowed : 18.30 % Favored : 77.78 % 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: -2.12 (0.42), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR L 39 PHE 0.012 0.003 PHE G 94 HIS 0.005 0.003 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 3036) covalent geometry : angle 0.50400 ( 4092) hydrogen bonds : bond 0.02110 ( 30) hydrogen bonds : angle 4.14933 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.070 Fit side-chains REVERT: K 60 LYS cc_start: 0.7892 (tttt) cc_final: 0.7611 (tttm) REVERT: G 60 LYS cc_start: 0.7778 (tttt) cc_final: 0.7452 (tttp) REVERT: L 60 LYS cc_start: 0.7759 (tttt) cc_final: 0.7381 (tttm) REVERT: M 43 LYS cc_start: 0.8345 (mtpm) cc_final: 0.8129 (mttp) REVERT: M 60 LYS cc_start: 0.8213 (tttt) cc_final: 0.7738 (tttp) REVERT: O 60 LYS cc_start: 0.8231 (tttt) cc_final: 0.7731 (tttp) outliers start: 12 outliers final: 11 residues processed: 45 average time/residue: 0.3252 time to fit residues: 15.1676 Evaluate side-chains 44 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.4540 r_free = 0.4540 target = 0.170752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.128379 restraints weight = 3125.697| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 2.28 r_work: 0.3984 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3844 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.036 3036 Z= 0.376 Angle : 0.708 4.827 4092 Z= 0.407 Chirality : 0.059 0.144 540 Planarity : 0.003 0.009 504 Dihedral : 5.212 14.195 432 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.08 % Favored : 87.92 % Rotamer: Outliers : 5.88 % Allowed : 16.67 % Favored : 77.45 % 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: -2.21 (0.41), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR L 39 PHE 0.018 0.005 PHE G 94 HIS 0.006 0.004 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.00831 ( 3036) covalent geometry : angle 0.70763 ( 4092) hydrogen bonds : bond 0.02727 ( 30) hydrogen bonds : angle 4.26297 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.117 Fit side-chains REVERT: K 60 LYS cc_start: 0.7882 (tttt) cc_final: 0.7587 (tttm) REVERT: G 60 LYS cc_start: 0.7822 (tttt) cc_final: 0.7487 (tttm) REVERT: L 60 LYS cc_start: 0.7786 (tttt) cc_final: 0.7396 (tttm) REVERT: M 43 LYS cc_start: 0.8375 (mtpm) cc_final: 0.8119 (mtpt) REVERT: M 60 LYS cc_start: 0.8267 (tttt) cc_final: 0.7972 (tttp) outliers start: 18 outliers final: 15 residues processed: 55 average time/residue: 0.3538 time to fit residues: 20.1905 Evaluate side-chains 54 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 0.0980 chunk 21 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 28 optimal weight: 30.0000 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.4646 r_free = 0.4646 target = 0.179161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.142498 restraints weight = 3270.794| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 2.11 r_work: 0.4107 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3968 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3036 Z= 0.113 Angle : 0.454 3.594 4092 Z= 0.257 Chirality : 0.052 0.138 540 Planarity : 0.001 0.005 504 Dihedral : 4.322 12.578 432 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.92 % Allowed : 18.95 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.98 (0.42), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR O 39 PHE 0.009 0.002 PHE G 94 HIS 0.004 0.002 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 3036) covalent geometry : angle 0.45377 ( 4092) hydrogen bonds : bond 0.01869 ( 30) hydrogen bonds : angle 3.94760 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.118 Fit side-chains REVERT: K 60 LYS cc_start: 0.7852 (tttt) cc_final: 0.7575 (tttm) REVERT: G 60 LYS cc_start: 0.7789 (tttt) cc_final: 0.7478 (tttm) REVERT: L 60 LYS cc_start: 0.7736 (tttt) cc_final: 0.7349 (tttm) REVERT: M 43 LYS cc_start: 0.8323 (mtpm) cc_final: 0.7844 (mttp) REVERT: M 60 LYS cc_start: 0.8184 (tttt) cc_final: 0.7709 (tttp) REVERT: O 60 LYS cc_start: 0.8206 (tttt) cc_final: 0.7687 (tttp) outliers start: 12 outliers final: 11 residues processed: 43 average time/residue: 0.4811 time to fit residues: 21.3353 Evaluate side-chains 41 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 0.0980 chunk 11 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 16 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4660 r_free = 0.4660 target = 0.181553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.144172 restraints weight = 3224.011| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 2.15 r_work: 0.4129 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3992 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3036 Z= 0.098 Angle : 0.428 3.391 4092 Z= 0.243 Chirality : 0.051 0.135 540 Planarity : 0.001 0.005 504 Dihedral : 4.033 12.136 432 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.92 % Allowed : 18.63 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.42), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR O 39 PHE 0.009 0.002 PHE O 94 HIS 0.004 0.002 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 3036) covalent geometry : angle 0.42815 ( 4092) hydrogen bonds : bond 0.01738 ( 30) hydrogen bonds : angle 3.72651 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 0.068 Fit side-chains REVERT: K 60 LYS cc_start: 0.7883 (tttt) cc_final: 0.7615 (tttm) REVERT: G 60 LYS cc_start: 0.7759 (tttt) cc_final: 0.7442 (tttm) REVERT: L 43 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7789 (mtpt) REVERT: L 60 LYS cc_start: 0.7743 (tttt) cc_final: 0.7378 (tttm) REVERT: M 43 LYS cc_start: 0.8323 (mtpm) cc_final: 0.8018 (mtpt) REVERT: M 60 LYS cc_start: 0.8197 (tttt) cc_final: 0.7723 (tttp) outliers start: 12 outliers final: 11 residues processed: 40 average time/residue: 0.3420 time to fit residues: 14.0989 Evaluate side-chains 40 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 40.0000 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.4610 r_free = 0.4610 target = 0.176900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.138556 restraints weight = 3162.933| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 2.14 r_work: 0.4060 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3925 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3036 Z= 0.198 Angle : 0.524 3.800 4092 Z= 0.298 Chirality : 0.053 0.137 540 Planarity : 0.002 0.007 504 Dihedral : 4.527 12.934 432 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.92 % Allowed : 19.28 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.42), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR L 39 PHE 0.013 0.003 PHE G 94 HIS 0.005 0.003 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 3036) covalent geometry : angle 0.52393 ( 4092) hydrogen bonds : bond 0.02090 ( 30) hydrogen bonds : angle 3.75103 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.068 Fit side-chains REVERT: K 60 LYS cc_start: 0.7910 (tttt) cc_final: 0.7634 (tttm) REVERT: G 60 LYS cc_start: 0.7800 (tttt) cc_final: 0.7476 (tttm) REVERT: L 60 LYS cc_start: 0.7720 (tttt) cc_final: 0.7343 (tttp) REVERT: M 43 LYS cc_start: 0.8346 (mtpm) cc_final: 0.8129 (mttp) REVERT: M 60 LYS cc_start: 0.8224 (tttt) cc_final: 0.7759 (tttp) REVERT: O 60 LYS cc_start: 0.8257 (tttt) cc_final: 0.7769 (tttp) outliers start: 12 outliers final: 12 residues processed: 43 average time/residue: 0.3064 time to fit residues: 13.6299 Evaluate side-chains 44 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 30.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.4561 r_free = 0.4561 target = 0.172721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.130702 restraints weight = 3080.128| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 2.27 r_work: 0.4010 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3872 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 3036 Z= 0.294 Angle : 0.625 4.260 4092 Z= 0.357 Chirality : 0.056 0.140 540 Planarity : 0.002 0.008 504 Dihedral : 4.943 13.505 432 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 4.25 % Allowed : 18.95 % Favored : 76.80 % 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: -1.94 (0.42), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR L 39 PHE 0.016 0.004 PHE G 94 HIS 0.006 0.004 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.00652 ( 3036) covalent geometry : angle 0.62461 ( 4092) hydrogen bonds : bond 0.02423 ( 30) hydrogen bonds : angle 3.93278 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1341.72 seconds wall clock time: 23 minutes 34.15 seconds (1414.15 seconds total)