Starting phenix.real_space_refine on Fri Aug 22 13:04:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hzb_35087/08_2025/8hzb_35087.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hzb_35087/08_2025/8hzb_35087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hzb_35087/08_2025/8hzb_35087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hzb_35087/08_2025/8hzb_35087.map" model { file = "/net/cci-nas-00/data/ceres_data/8hzb_35087/08_2025/8hzb_35087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hzb_35087/08_2025/8hzb_35087.cif" } resolution = 3.2 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 1860 2.51 5 N 516 2.21 5 O 600 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2976 Number of models: 1 Model: "" Number of chains: 1 Chain: "D" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 496 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain breaks: 1 Restraints were copied for chains: C, E, F, A, B Time building chain proxies: 0.76, per 1000 atoms: 0.26 Number of scatterers: 2976 At special positions: 0 Unit cell: (96.28, 121.18, 36.52, 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 600 8.00 N 516 7.00 C 1860 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 78.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 50.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 15 through 21 removed outlier: 6.545A pdb=" N VAL D 16 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N ALA E 19 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA D 18 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LYS E 21 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU D 20 " --> pdb=" O LYS E 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 58 removed outlier: 6.799A pdb=" N GLY C 47 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL D 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA C 53 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR D 54 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C 55 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA D 56 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLU C 57 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL D 48 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL E 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N HIS D 50 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLY E 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 62 through 66 removed outlier: 6.526A pdb=" N VAL D 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL E 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN D 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 69 through 80 removed outlier: 9.129A pdb=" N VAL D 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 10.489A pdb=" N GLY C 73 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR D 72 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N THR C 75 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL D 74 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL C 77 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ALA D 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 10.130A pdb=" N GLN C 79 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N ALA D 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL E 70 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL D 71 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR E 72 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLY D 73 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL D 77 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA E 78 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN D 79 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS E 80 " --> pdb=" O GLN D 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.784A pdb=" N PHE C 94 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N THR D 92 " --> pdb=" O GLY E 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 97 through 98 removed outlier: 6.906A pdb=" N LYS D 97 " --> pdb=" O ASP E 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 15 through 21 removed outlier: 6.526A pdb=" N VAL F 16 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N ALA B 19 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA F 18 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N LYS B 21 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLU F 20 " --> pdb=" O LYS B 21 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 46 through 58 removed outlier: 6.821A pdb=" N GLY A 47 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL F 52 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA A 53 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR F 54 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A 55 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA F 56 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLU A 57 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL F 48 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL B 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N HIS F 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY B 51 " --> pdb=" O HIS F 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 62 through 66 removed outlier: 6.572A pdb=" N VAL F 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL B 66 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASN F 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 69 through 80 removed outlier: 9.115A pdb=" N VAL F 70 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 10.470A pdb=" N GLY A 73 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR F 72 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N THR A 75 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL F 74 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL A 77 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ALA F 76 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N GLN A 79 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N ALA F 78 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL B 70 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL F 71 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR B 72 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY F 73 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL F 77 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA B 78 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLN F 79 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS B 80 " --> pdb=" O GLN F 79 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 91 through 94 removed outlier: 6.805A pdb=" N PHE A 94 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N THR F 92 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 97 through 98 removed outlier: 6.896A pdb=" N LYS F 97 " --> pdb=" O ASP B 98 " (cutoff:3.500A) 54 hydrogen bonds defined for protein. 162 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: 0.45 Time building geometry restraints manager: 0.29 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: 528 1.29 - 1.35: 460 1.35 - 1.42: 102 1.42 - 1.48: 501 1.48 - 1.55: 1391 Bond restraints: 2982 Sorted by residual: bond pdb=" CA LYS A 58 " pdb=" C LYS A 58 " ideal model delta sigma weight residual 1.526 1.510 0.016 1.08e-02 8.57e+03 2.16e+00 bond pdb=" CA LYS E 58 " pdb=" C LYS E 58 " ideal model delta sigma weight residual 1.526 1.510 0.016 1.08e-02 8.57e+03 2.07e+00 bond pdb=" CA LYS C 58 " pdb=" C LYS C 58 " ideal model delta sigma weight residual 1.526 1.511 0.015 1.08e-02 8.57e+03 1.95e+00 bond pdb=" CA LYS B 58 " pdb=" C LYS B 58 " ideal model delta sigma weight residual 1.526 1.511 0.015 1.08e-02 8.57e+03 1.94e+00 bond pdb=" CA LYS D 58 " pdb=" C LYS D 58 " ideal model delta sigma weight residual 1.526 1.511 0.015 1.08e-02 8.57e+03 1.92e+00 ... (remaining 2977 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 3486 1.14 - 2.28: 412 2.28 - 3.42: 93 3.42 - 4.56: 23 4.56 - 5.70: 12 Bond angle restraints: 4026 Sorted by residual: angle pdb=" C GLY E 41 " pdb=" N SER E 42 " pdb=" CA SER E 42 " ideal model delta sigma weight residual 122.42 117.96 4.46 1.55e+00 4.16e-01 8.26e+00 angle pdb=" C GLY A 41 " pdb=" N SER A 42 " pdb=" CA SER A 42 " ideal model delta sigma weight residual 122.42 117.97 4.45 1.55e+00 4.16e-01 8.24e+00 angle pdb=" C GLY B 41 " pdb=" N SER B 42 " pdb=" CA SER B 42 " ideal model delta sigma weight residual 122.42 117.97 4.45 1.55e+00 4.16e-01 8.23e+00 angle pdb=" C GLY D 41 " pdb=" N SER D 42 " pdb=" CA SER D 42 " ideal model delta sigma weight residual 122.42 117.97 4.45 1.55e+00 4.16e-01 8.23e+00 angle pdb=" C GLY C 41 " pdb=" N SER C 42 " pdb=" CA SER C 42 " ideal model delta sigma weight residual 122.42 118.01 4.41 1.55e+00 4.16e-01 8.11e+00 ... (remaining 4021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 1524 17.62 - 35.24: 186 35.24 - 52.85: 30 52.85 - 70.47: 0 70.47 - 88.09: 12 Dihedral angle restraints: 1752 sinusoidal: 582 harmonic: 1170 Sorted by residual: dihedral pdb=" CA VAL A 40 " pdb=" C VAL A 40 " pdb=" N GLY A 41 " pdb=" CA GLY A 41 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA VAL D 40 " pdb=" C VAL D 40 " pdb=" N GLY D 41 " pdb=" CA GLY D 41 " ideal model delta harmonic sigma weight residual 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA VAL F 40 " pdb=" C VAL F 40 " pdb=" N GLY F 41 " pdb=" CA GLY F 41 " ideal model delta harmonic sigma weight residual 180.00 156.45 23.55 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 1749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 148 0.026 - 0.051: 160 0.051 - 0.077: 99 0.077 - 0.102: 71 0.102 - 0.128: 56 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA VAL F 49 " pdb=" N VAL F 49 " pdb=" C VAL F 49 " pdb=" CB VAL F 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA VAL E 49 " pdb=" N VAL E 49 " pdb=" C VAL E 49 " pdb=" CB VAL E 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 531 not shown) Planarity restraints: 498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 66 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C VAL C 66 " -0.024 2.00e-02 2.50e+03 pdb=" O VAL C 66 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY C 67 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 66 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.86e+00 pdb=" C VAL E 66 " -0.024 2.00e-02 2.50e+03 pdb=" O VAL E 66 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY E 67 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 66 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.81e+00 pdb=" C VAL B 66 " 0.023 2.00e-02 2.50e+03 pdb=" O VAL B 66 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY B 67 " -0.008 2.00e-02 2.50e+03 ... (remaining 495 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 154 2.71 - 3.26: 2853 3.26 - 3.80: 4388 3.80 - 4.35: 5053 4.35 - 4.90: 10336 Nonbonded interactions: 22784 Sorted by model distance: nonbonded pdb=" OE2 GLU F 46 " pdb=" NZ LYS F 80 " model vdw 2.162 3.120 nonbonded pdb=" OE2 GLU C 46 " pdb=" NZ LYS C 80 " model vdw 2.162 3.120 nonbonded pdb=" OE2 GLU E 46 " pdb=" NZ LYS E 80 " model vdw 2.162 3.120 nonbonded pdb=" OE2 GLU B 46 " pdb=" NZ LYS B 80 " model vdw 2.162 3.120 nonbonded pdb=" OE2 GLU A 46 " pdb=" NZ LYS A 80 " model vdw 2.162 3.120 ... (remaining 22779 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 'C' selection = chain 'E' selection = chain 'F' selection = chain 'A' selection = chain 'B' } 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: 5.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.160 Find NCS groups from input model: 0.030 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:1.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 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 0.044 2982 Z= 0.398 Angle : 0.920 5.699 4026 Z= 0.518 Chirality : 0.059 0.128 534 Planarity : 0.004 0.014 498 Dihedral : 16.623 88.088 1008 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % 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 aren not related in a simple way. whole: -4.16 (0.28), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.22), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.005 TYR F 39 PHE 0.019 0.006 PHE C 94 HIS 0.005 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00807 ( 2982) covalent geometry : angle 0.92012 ( 4026) hydrogen bonds : bond 0.18721 ( 54) hydrogen bonds : angle 8.50467 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.115 Fit side-chains REVERT: C 45 LYS cc_start: 0.7387 (tttt) cc_final: 0.7140 (tttm) REVERT: E 45 LYS cc_start: 0.7543 (tttt) cc_final: 0.7095 (tttm) REVERT: F 45 LYS cc_start: 0.7570 (tttt) cc_final: 0.7092 (tttm) REVERT: A 45 LYS cc_start: 0.7425 (tttt) cc_final: 0.7175 (tttm) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0937 time to fit residues: 2.6158 Evaluate side-chains 23 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.114 ------------------------------------------------------------------------------- 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: 0.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.9188 ------------------------------------------------------------------------------- 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 = 0.5065 r_free = 0.5065 target = 0.257967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.221858 restraints weight = 3347.753| |-----------------------------------------------------------------------------| r_work (start): 0.4744 rms_B_bonded: 2.91 r_work: 0.4653 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2982 Z= 0.113 Angle : 0.572 4.753 4026 Z= 0.310 Chirality : 0.051 0.131 534 Planarity : 0.002 0.012 498 Dihedral : 6.008 22.039 426 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 2.00 % Allowed : 24.67 % Favored : 73.33 % 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 aren not related in a simple way. whole: -3.37 (0.35), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR A 39 PHE 0.005 0.001 PHE B 94 HIS 0.007 0.002 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 2982) covalent geometry : angle 0.57221 ( 4026) hydrogen bonds : bond 0.01939 ( 54) hydrogen bonds : angle 6.23665 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.119 Fit side-chains REVERT: E 45 LYS cc_start: 0.7624 (tttt) cc_final: 0.7047 (tttm) REVERT: A 39 TYR cc_start: 0.6866 (m-80) cc_final: 0.6309 (m-80) REVERT: B 45 LYS cc_start: 0.7410 (tttt) cc_final: 0.6882 (tttm) outliers start: 6 outliers final: 6 residues processed: 24 average time/residue: 0.0544 time to fit residues: 1.7871 Evaluate side-chains 24 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 11 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN C 65 ASN F 65 ASN A 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5015 r_free = 0.5015 target = 0.252179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.215899 restraints weight = 3374.174| |-----------------------------------------------------------------------------| r_work (start): 0.4641 rms_B_bonded: 2.83 r_work: 0.4550 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2982 Z= 0.198 Angle : 0.690 5.497 4026 Z= 0.370 Chirality : 0.052 0.128 534 Planarity : 0.003 0.013 498 Dihedral : 6.564 21.376 426 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 5.33 % Allowed : 22.33 % Favored : 72.33 % 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 aren not related in a simple way. whole: -3.22 (0.36), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR C 39 PHE 0.012 0.004 PHE E 94 HIS 0.007 0.003 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 2982) covalent geometry : angle 0.69001 ( 4026) hydrogen bonds : bond 0.02203 ( 54) hydrogen bonds : angle 5.88618 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 21 time to evaluate : 0.134 Fit side-chains REVERT: D 39 TYR cc_start: 0.6978 (m-80) cc_final: 0.6707 (m-80) REVERT: E 44 THR cc_start: 0.7038 (OUTLIER) cc_final: 0.6763 (t) REVERT: E 45 LYS cc_start: 0.7728 (tttt) cc_final: 0.7188 (tttm) REVERT: F 44 THR cc_start: 0.6844 (OUTLIER) cc_final: 0.6535 (t) REVERT: A 44 THR cc_start: 0.6854 (OUTLIER) cc_final: 0.6553 (t) REVERT: B 39 TYR cc_start: 0.7137 (m-80) cc_final: 0.6904 (m-80) REVERT: B 44 THR cc_start: 0.6802 (OUTLIER) cc_final: 0.6537 (t) REVERT: B 45 LYS cc_start: 0.7533 (tttt) cc_final: 0.7094 (tttm) outliers start: 16 outliers final: 10 residues processed: 34 average time/residue: 0.0396 time to fit residues: 1.9208 Evaluate side-chains 36 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 22 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 66 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.5047 r_free = 0.5047 target = 0.253853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.219014 restraints weight = 3313.681| |-----------------------------------------------------------------------------| r_work (start): 0.4742 rms_B_bonded: 2.87 r_work: 0.4647 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2982 Z= 0.097 Angle : 0.521 4.459 4026 Z= 0.282 Chirality : 0.051 0.134 534 Planarity : 0.002 0.012 498 Dihedral : 5.408 19.693 426 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 6.00 % Allowed : 23.33 % Favored : 70.67 % 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 aren not related in a simple way. whole: -2.97 (0.38), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR C 39 PHE 0.006 0.002 PHE B 94 HIS 0.005 0.002 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00188 ( 2982) covalent geometry : angle 0.52080 ( 4026) hydrogen bonds : bond 0.01645 ( 54) hydrogen bonds : angle 5.70841 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 17 time to evaluate : 0.072 Fit side-chains REVERT: E 44 THR cc_start: 0.6801 (OUTLIER) cc_final: 0.6590 (t) REVERT: E 45 LYS cc_start: 0.7708 (tttt) cc_final: 0.7134 (tttm) REVERT: A 39 TYR cc_start: 0.6832 (m-80) cc_final: 0.6384 (m-80) REVERT: B 45 LYS cc_start: 0.7564 (tttt) cc_final: 0.6996 (tttm) outliers start: 18 outliers final: 10 residues processed: 35 average time/residue: 0.0531 time to fit residues: 2.4209 Evaluate side-chains 26 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 15 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 chunk 29 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 15 optimal weight: 0.2980 chunk 10 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- 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 = 0.4999 r_free = 0.4999 target = 0.249196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.212765 restraints weight = 3328.197| |-----------------------------------------------------------------------------| r_work (start): 0.4603 rms_B_bonded: 2.80 r_work: 0.4511 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 2982 Z= 0.279 Angle : 0.790 7.400 4026 Z= 0.424 Chirality : 0.056 0.216 534 Planarity : 0.003 0.014 498 Dihedral : 7.037 20.472 426 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Rotamer: Outliers : 7.67 % Allowed : 21.67 % Favored : 70.67 % 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 aren not related in a simple way. whole: -3.14 (0.36), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.005 TYR C 39 PHE 0.017 0.005 PHE B 94 HIS 0.007 0.003 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00612 ( 2982) covalent geometry : angle 0.79017 ( 4026) hydrogen bonds : bond 0.02384 ( 54) hydrogen bonds : angle 5.77713 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 23 time to evaluate : 0.080 Fit side-chains REVERT: D 39 TYR cc_start: 0.7087 (m-80) cc_final: 0.6851 (m-80) REVERT: E 39 TYR cc_start: 0.7187 (m-80) cc_final: 0.6985 (m-80) REVERT: E 44 THR cc_start: 0.6913 (OUTLIER) cc_final: 0.6666 (t) REVERT: E 45 LYS cc_start: 0.7796 (tttt) cc_final: 0.7296 (tttm) REVERT: F 39 TYR cc_start: 0.7095 (m-80) cc_final: 0.6854 (m-80) REVERT: B 45 LYS cc_start: 0.7740 (tttt) cc_final: 0.7342 (tttm) outliers start: 23 outliers final: 15 residues processed: 42 average time/residue: 0.0402 time to fit residues: 2.2651 Evaluate side-chains 39 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 23 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 8 optimal weight: 0.4980 chunk 21 optimal weight: 30.0000 chunk 23 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.5074 r_free = 0.5074 target = 0.258317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.223583 restraints weight = 3360.743| |-----------------------------------------------------------------------------| r_work (start): 0.4711 rms_B_bonded: 2.79 r_work: 0.4615 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2982 Z= 0.109 Angle : 0.557 4.578 4026 Z= 0.299 Chirality : 0.051 0.178 534 Planarity : 0.002 0.012 498 Dihedral : 5.685 20.004 426 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 3.33 % Allowed : 25.33 % Favored : 71.33 % 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 aren not related in a simple way. whole: -2.97 (0.37), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR C 39 PHE 0.007 0.002 PHE B 94 HIS 0.005 0.002 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 2982) covalent geometry : angle 0.55682 ( 4026) hydrogen bonds : bond 0.01696 ( 54) hydrogen bonds : angle 5.71428 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 17 time to evaluate : 0.114 Fit side-chains REVERT: C 39 TYR cc_start: 0.6921 (m-80) cc_final: 0.6483 (m-80) REVERT: E 44 THR cc_start: 0.6798 (OUTLIER) cc_final: 0.6569 (t) REVERT: E 45 LYS cc_start: 0.7782 (tttt) cc_final: 0.7214 (tttm) REVERT: A 39 TYR cc_start: 0.6891 (m-80) cc_final: 0.6360 (m-80) REVERT: B 45 LYS cc_start: 0.7698 (tttt) cc_final: 0.7228 (tttm) outliers start: 10 outliers final: 8 residues processed: 27 average time/residue: 0.0420 time to fit residues: 1.5429 Evaluate side-chains 26 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 17 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 81 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 0.0980 chunk 5 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 29 optimal weight: 0.4980 chunk 22 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.0010 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 = 0.5110 r_free = 0.5110 target = 0.261926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.227479 restraints weight = 3416.189| |-----------------------------------------------------------------------------| r_work (start): 0.4765 rms_B_bonded: 2.74 r_work: 0.4659 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 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 0.018 2982 Z= 0.089 Angle : 0.503 4.930 4026 Z= 0.272 Chirality : 0.050 0.158 534 Planarity : 0.002 0.012 498 Dihedral : 5.135 18.077 426 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 3.67 % Allowed : 24.33 % Favored : 72.00 % 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 aren not related in a simple way. whole: -2.82 (0.39), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR C 39 PHE 0.004 0.001 PHE B 94 HIS 0.005 0.002 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00175 ( 2982) covalent geometry : angle 0.50345 ( 4026) hydrogen bonds : bond 0.01515 ( 54) hydrogen bonds : angle 5.54595 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 11 time to evaluate : 0.067 Fit side-chains REVERT: B 45 LYS cc_start: 0.7675 (tttt) cc_final: 0.7242 (tttm) outliers start: 11 outliers final: 9 residues processed: 21 average time/residue: 0.0237 time to fit residues: 0.7654 Evaluate side-chains 20 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 11 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 = 0.5003 r_free = 0.5003 target = 0.248570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.212408 restraints weight = 3341.814| |-----------------------------------------------------------------------------| r_work (start): 0.4606 rms_B_bonded: 2.73 r_work: 0.4506 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 2982 Z= 0.259 Angle : 0.758 7.360 4026 Z= 0.404 Chirality : 0.054 0.131 534 Planarity : 0.003 0.014 498 Dihedral : 6.861 20.221 426 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 4.67 % Allowed : 22.67 % Favored : 72.67 % 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 aren not related in a simple way. whole: -2.87 (0.37), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.004 TYR C 39 PHE 0.017 0.005 PHE B 94 HIS 0.007 0.003 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00558 ( 2982) covalent geometry : angle 0.75785 ( 4026) hydrogen bonds : bond 0.02310 ( 54) hydrogen bonds : angle 5.67188 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 20 time to evaluate : 0.063 Fit side-chains REVERT: E 45 LYS cc_start: 0.7779 (tttt) cc_final: 0.7263 (tttm) REVERT: B 45 LYS cc_start: 0.7718 (tttt) cc_final: 0.7273 (tttm) outliers start: 14 outliers final: 13 residues processed: 29 average time/residue: 0.0304 time to fit residues: 1.2787 Evaluate side-chains 33 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 20 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.5057 r_free = 0.5057 target = 0.255610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.220822 restraints weight = 3396.581| |-----------------------------------------------------------------------------| r_work (start): 0.4696 rms_B_bonded: 2.79 r_work: 0.4604 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2982 Z= 0.113 Angle : 0.562 5.015 4026 Z= 0.301 Chirality : 0.051 0.146 534 Planarity : 0.002 0.012 498 Dihedral : 5.718 18.112 426 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 4.33 % Allowed : 23.33 % Favored : 72.33 % 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 aren not related in a simple way. whole: -2.79 (0.38), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.002 TYR F 39 PHE 0.005 0.002 PHE B 94 HIS 0.006 0.002 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 2982) covalent geometry : angle 0.56225 ( 4026) hydrogen bonds : bond 0.01664 ( 54) hydrogen bonds : angle 5.58223 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 15 time to evaluate : 0.061 Fit side-chains REVERT: B 45 LYS cc_start: 0.7666 (tttt) cc_final: 0.7227 (tttm) outliers start: 13 outliers final: 12 residues processed: 26 average time/residue: 0.0272 time to fit residues: 1.0270 Evaluate side-chains 27 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 15 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 5.9990 chunk 9 optimal weight: 0.4980 chunk 7 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 0.0040 chunk 18 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.4996 ------------------------------------------------------------------------------- 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 = 0.5053 r_free = 0.5053 target = 0.254530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.219054 restraints weight = 3402.952| |-----------------------------------------------------------------------------| r_work (start): 0.4675 rms_B_bonded: 2.80 r_work: 0.4583 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2982 Z= 0.130 Angle : 0.578 5.072 4026 Z= 0.308 Chirality : 0.051 0.134 534 Planarity : 0.002 0.013 498 Dihedral : 5.783 17.268 426 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.01 % Favored : 87.99 % Rotamer: Outliers : 4.00 % Allowed : 23.33 % Favored : 72.67 % 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 aren not related in a simple way. whole: -2.75 (0.38), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR F 39 PHE 0.008 0.002 PHE B 94 HIS 0.006 0.002 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 2982) covalent geometry : angle 0.57759 ( 4026) hydrogen bonds : bond 0.01685 ( 54) hydrogen bonds : angle 5.55149 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 16 time to evaluate : 0.083 Fit side-chains REVERT: E 45 LYS cc_start: 0.7691 (tttt) cc_final: 0.7161 (tttm) REVERT: B 45 LYS cc_start: 0.7704 (tttt) cc_final: 0.7222 (tttm) outliers start: 12 outliers final: 12 residues processed: 26 average time/residue: 0.0398 time to fit residues: 1.4243 Evaluate side-chains 28 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 16 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 10.0000 chunk 29 optimal weight: 0.0030 chunk 27 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 32 optimal weight: 0.0770 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 20.0000 chunk 36 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 overall best weight: 0.4748 ------------------------------------------------------------------------------- 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 = 0.5120 r_free = 0.5120 target = 0.262394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.228828 restraints weight = 3303.783| |-----------------------------------------------------------------------------| r_work (start): 0.4838 rms_B_bonded: 2.58 r_work: 0.4747 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2982 Z= 0.078 Angle : 0.475 3.933 4026 Z= 0.259 Chirality : 0.050 0.138 534 Planarity : 0.002 0.012 498 Dihedral : 4.855 14.774 426 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 2.33 % Allowed : 25.00 % Favored : 72.67 % 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 aren not related in a simple way. whole: -2.60 (0.39), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR E 39 PHE 0.002 0.001 PHE B 94 HIS 0.004 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00157 ( 2982) covalent geometry : angle 0.47550 ( 4026) hydrogen bonds : bond 0.01480 ( 54) hydrogen bonds : angle 5.45223 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 869.92 seconds wall clock time: 15 minutes 36.80 seconds (936.80 seconds total)