Starting phenix.real_space_refine on Fri Aug 22 12:57:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yk2_33884/08_2025/7yk2_33884.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yk2_33884/08_2025/7yk2_33884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yk2_33884/08_2025/7yk2_33884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yk2_33884/08_2025/7yk2_33884.map" model { file = "/net/cci-nas-00/data/ceres_data/7yk2_33884/08_2025/7yk2_33884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yk2_33884/08_2025/7yk2_33884.cif" } resolution = 2.8 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= 0.003 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 1644 2.51 5 N 456 2.21 5 O 528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 2628 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" 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: D, E, A, F, B Time building chain proxies: 0.43, per 1000 atoms: 0.16 Number of scatterers: 2628 At special positions: 0 Unit cell: (98.58, 117.66, 31.8, 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 528 8.00 N 456 7.00 C 1644 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: 0.12 Conformation dependent library (CDL) restraints added in 71.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 42.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 58 removed outlier: 8.665A pdb=" N GLU C 46 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N VAL F 49 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N VAL C 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 10.541A pdb=" N GLY F 51 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N HIS C 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N ALA F 53 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL C 52 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N VAL F 55 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR C 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLU F 57 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA C 56 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL F 48 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL E 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS F 50 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLY E 51 " --> pdb=" O HIS F 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 62 through 65 removed outlier: 6.908A pdb=" N GLN E 62 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ASN F 65 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR E 64 " --> pdb=" O ASN F 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 71 through 82 removed outlier: 8.999A pdb=" N VAL C 71 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N VAL F 74 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY C 73 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ALA F 76 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N THR C 75 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ALA F 78 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N VAL C 77 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 10.641A pdb=" N LYS F 80 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N GLN C 79 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 10.364A pdb=" N VAL F 82 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N THR C 81 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR E 72 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY F 73 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL F 77 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA E 78 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLN F 79 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LYS E 80 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR F 81 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL E 82 " --> pdb=" O THR F 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 86 through 87 removed outlier: 6.238A pdb=" N GLY E 86 " --> pdb=" O SER F 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 46 through 58 removed outlier: 8.658A pdb=" N GLU D 46 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N VAL B 49 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 9.164A pdb=" N VAL D 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 10.542A pdb=" N GLY B 51 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N HIS D 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N ALA B 53 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL D 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N VAL B 55 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR D 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N GLU B 57 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA D 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL B 48 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A 49 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N HIS B 50 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLY A 51 " --> pdb=" O HIS B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 62 through 65 removed outlier: 6.271A pdb=" N VAL D 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLN A 62 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ASN B 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR A 64 " --> pdb=" O ASN B 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 71 through 82 removed outlier: 6.919A pdb=" N THR B 72 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY D 73 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL D 77 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA B 78 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN D 79 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS B 80 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR D 81 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL B 82 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR A 72 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY B 73 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 77 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ALA A 78 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLN B 79 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS A 80 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR B 81 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL A 82 " --> pdb=" O THR B 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 86 through 87 removed outlier: 6.234A pdb=" N GLY A 86 " --> pdb=" O SER B 87 " (cutoff:3.500A) 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: 0.20 Time building geometry restraints manager: 0.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 462 1.29 - 1.35: 414 1.35 - 1.42: 102 1.42 - 1.48: 426 1.48 - 1.55: 1236 Bond restraints: 2640 Sorted by residual: bond pdb=" CG LEU D 38 " pdb=" CD1 LEU D 38 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.21e+00 bond pdb=" CG LEU A 38 " pdb=" CD1 LEU A 38 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CG LEU F 38 " pdb=" CD1 LEU F 38 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CG LEU B 38 " pdb=" CD1 LEU B 38 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.19e+00 bond pdb=" CG LEU C 38 " pdb=" CD1 LEU C 38 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.18e+00 ... (remaining 2635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.89: 2905 0.89 - 1.77: 475 1.77 - 2.66: 129 2.66 - 3.55: 49 3.55 - 4.43: 12 Bond angle restraints: 3570 Sorted by residual: angle pdb=" CA ILE B 88 " pdb=" C ILE B 88 " pdb=" N ALA B 89 " ideal model delta sigma weight residual 117.15 119.77 -2.62 7.80e-01 1.64e+00 1.13e+01 angle pdb=" CA ILE A 88 " pdb=" C ILE A 88 " pdb=" N ALA A 89 " ideal model delta sigma weight residual 117.15 119.75 -2.60 7.80e-01 1.64e+00 1.11e+01 angle pdb=" CA ILE C 88 " pdb=" C ILE C 88 " pdb=" N ALA C 89 " ideal model delta sigma weight residual 117.15 119.75 -2.60 7.80e-01 1.64e+00 1.11e+01 angle pdb=" CA ILE F 88 " pdb=" C ILE F 88 " pdb=" N ALA F 89 " ideal model delta sigma weight residual 117.15 119.74 -2.59 7.80e-01 1.64e+00 1.11e+01 angle pdb=" CA ILE D 88 " pdb=" C ILE D 88 " pdb=" N ALA D 89 " ideal model delta sigma weight residual 117.15 119.74 -2.59 7.80e-01 1.64e+00 1.10e+01 ... (remaining 3565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.30: 1308 10.30 - 20.60: 162 20.60 - 30.90: 54 30.90 - 41.20: 18 41.20 - 51.50: 6 Dihedral angle restraints: 1548 sinusoidal: 522 harmonic: 1026 Sorted by residual: dihedral pdb=" CA TYR E 39 " pdb=" CB TYR E 39 " pdb=" CG TYR E 39 " pdb=" CD1 TYR E 39 " ideal model delta sinusoidal sigma weight residual -20.00 31.50 -51.50 2 2.00e+01 2.50e-03 7.35e+00 dihedral pdb=" CA TYR F 39 " pdb=" CB TYR F 39 " pdb=" CG TYR F 39 " pdb=" CD1 TYR F 39 " ideal model delta sinusoidal sigma weight residual -20.00 31.42 -51.42 2 2.00e+01 2.50e-03 7.33e+00 dihedral pdb=" CA TYR B 39 " pdb=" CB TYR B 39 " pdb=" CG TYR B 39 " pdb=" CD1 TYR B 39 " ideal model delta sinusoidal sigma weight residual -20.00 31.40 -51.40 2 2.00e+01 2.50e-03 7.33e+00 ... (remaining 1545 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.027: 232 0.027 - 0.053: 120 0.053 - 0.080: 48 0.080 - 0.106: 39 0.106 - 0.132: 29 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA VAL A 70 " pdb=" N VAL A 70 " pdb=" C VAL A 70 " pdb=" CB VAL A 70 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA VAL E 70 " pdb=" N VAL E 70 " pdb=" C VAL E 70 " pdb=" CB VAL E 70 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA VAL F 70 " pdb=" N VAL F 70 " pdb=" C VAL F 70 " pdb=" CB VAL F 70 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 465 not shown) Planarity restraints: 444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 83 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" C GLU B 83 " 0.020 2.00e-02 2.50e+03 pdb=" O GLU B 83 " -0.008 2.00e-02 2.50e+03 pdb=" N GLY B 84 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 83 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.31e+00 pdb=" C GLU A 83 " 0.020 2.00e-02 2.50e+03 pdb=" O GLU A 83 " -0.008 2.00e-02 2.50e+03 pdb=" N GLY A 84 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 83 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.31e+00 pdb=" C GLU D 83 " 0.020 2.00e-02 2.50e+03 pdb=" O GLU D 83 " -0.008 2.00e-02 2.50e+03 pdb=" N GLY D 84 " -0.007 2.00e-02 2.50e+03 ... (remaining 441 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 1092 2.92 - 3.41: 2311 3.41 - 3.91: 3902 3.91 - 4.40: 4330 4.40 - 4.90: 8827 Nonbonded interactions: 20462 Sorted by model distance: nonbonded pdb=" NE2 GLN F 62 " pdb=" OG1 THR F 64 " model vdw 2.424 3.120 nonbonded pdb=" NE2 GLN E 62 " pdb=" OG1 THR E 64 " model vdw 2.424 3.120 nonbonded pdb=" NE2 GLN B 62 " pdb=" OG1 THR B 64 " model vdw 2.424 3.120 nonbonded pdb=" NE2 GLN A 62 " pdb=" OG1 THR A 64 " model vdw 2.425 3.120 nonbonded pdb=" NE2 GLN C 62 " pdb=" OG1 THR C 64 " model vdw 2.425 3.120 ... (remaining 20457 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 'C' selection = chain 'D' selection = chain 'E' selection = chain 'A' selection = chain 'F' 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: 1.500 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.900 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 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 : 0.005 0.036 2640 Z= 0.260 Angle : 0.816 4.432 3570 Z= 0.547 Chirality : 0.051 0.132 468 Planarity : 0.002 0.011 444 Dihedral : 11.384 51.497 900 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % 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: -3.89 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR C 39 PHE 0.013 0.004 PHE B 94 HIS 0.006 0.004 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 2640) covalent geometry : angle 0.81622 ( 3570) hydrogen bonds : bond 0.16252 ( 30) hydrogen bonds : angle 7.28354 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.057 Fit side-chains REVERT: C 80 LYS cc_start: 0.8084 (tttm) cc_final: 0.7741 (tttp) REVERT: F 83 GLU cc_start: 0.6983 (tm-30) cc_final: 0.6714 (tm-30) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.5419 time to fit residues: 28.1388 Evaluate side-chains 43 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN D 65 ASN E 65 ASN E 79 GLN A 65 ASN F 65 ASN B 65 ASN B 79 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.219240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.168842 restraints weight = 2510.955| |-----------------------------------------------------------------------------| r_work (start): 0.4413 rms_B_bonded: 2.59 r_work: 0.4290 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.4162 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2640 Z= 0.155 Angle : 0.548 3.506 3570 Z= 0.311 Chirality : 0.050 0.136 468 Planarity : 0.002 0.006 444 Dihedral : 4.799 12.425 378 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 1.48 % Allowed : 16.30 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR F 39 PHE 0.014 0.004 PHE D 94 HIS 0.006 0.003 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 2640) covalent geometry : angle 0.54798 ( 3570) hydrogen bonds : bond 0.02414 ( 30) hydrogen bonds : angle 5.03115 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.058 Fit side-chains REVERT: D 62 GLN cc_start: 0.7012 (tt0) cc_final: 0.6508 (tp40) REVERT: E 62 GLN cc_start: 0.6780 (tt0) cc_final: 0.6366 (tp40) REVERT: A 62 GLN cc_start: 0.7065 (tt0) cc_final: 0.6689 (tp40) REVERT: F 62 GLN cc_start: 0.6712 (tt0) cc_final: 0.6170 (tp40) REVERT: F 83 GLU cc_start: 0.7358 (tm-30) cc_final: 0.7096 (tm-30) outliers start: 4 outliers final: 3 residues processed: 49 average time/residue: 0.5822 time to fit residues: 29.1217 Evaluate side-chains 52 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 66 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN D 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.221829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.177367 restraints weight = 2690.800| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 2.28 r_work: 0.4248 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.4130 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 2640 Z= 0.253 Angle : 0.648 3.469 3570 Z= 0.373 Chirality : 0.053 0.132 468 Planarity : 0.003 0.009 444 Dihedral : 5.380 14.756 378 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.21 % Favored : 85.79 % Rotamer: Outliers : 5.93 % Allowed : 15.56 % Favored : 78.52 % 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 (0.39), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR B 39 PHE 0.020 0.006 PHE B 94 HIS 0.008 0.004 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 2640) covalent geometry : angle 0.64839 ( 3570) hydrogen bonds : bond 0.03005 ( 30) hydrogen bonds : angle 5.04966 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.083 Fit side-chains REVERT: E 43 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7402 (mptp) REVERT: A 62 GLN cc_start: 0.7044 (tt0) cc_final: 0.6660 (tp40) REVERT: F 83 GLU cc_start: 0.7374 (tm-30) cc_final: 0.7133 (tm-30) REVERT: B 57 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8260 (mt-10) REVERT: B 62 GLN cc_start: 0.7268 (tm-30) cc_final: 0.6955 (tm-30) outliers start: 16 outliers final: 9 residues processed: 55 average time/residue: 0.5639 time to fit residues: 31.6581 Evaluate side-chains 54 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 66 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.0170 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.221764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.171256 restraints weight = 2523.700| |-----------------------------------------------------------------------------| r_work (start): 0.4434 rms_B_bonded: 2.66 r_work: 0.4320 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.4196 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2640 Z= 0.110 Angle : 0.476 3.138 3570 Z= 0.271 Chirality : 0.050 0.131 468 Planarity : 0.002 0.007 444 Dihedral : 4.586 12.141 378 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 4.07 % Allowed : 17.04 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.75 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR E 39 PHE 0.010 0.003 PHE B 94 HIS 0.005 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 2640) covalent geometry : angle 0.47562 ( 3570) hydrogen bonds : bond 0.02105 ( 30) hydrogen bonds : angle 4.73324 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.072 Fit side-chains REVERT: D 46 GLU cc_start: 0.8139 (pt0) cc_final: 0.7841 (pt0) REVERT: D 60 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7505 (tttp) REVERT: E 43 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7266 (mptp) REVERT: E 62 GLN cc_start: 0.6911 (tt0) cc_final: 0.6061 (tp40) REVERT: A 62 GLN cc_start: 0.7192 (tt0) cc_final: 0.6892 (tp40) REVERT: F 83 GLU cc_start: 0.7362 (tm-30) cc_final: 0.7141 (tm-30) REVERT: B 57 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8366 (mt-10) REVERT: B 62 GLN cc_start: 0.7297 (tm-30) cc_final: 0.6884 (tm-30) outliers start: 11 outliers final: 6 residues processed: 52 average time/residue: 0.5284 time to fit residues: 28.0409 Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN E 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.219873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.168939 restraints weight = 2540.319| |-----------------------------------------------------------------------------| r_work (start): 0.4406 rms_B_bonded: 2.65 r_work: 0.4285 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.4159 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 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 : 0.003 0.027 2640 Z= 0.132 Angle : 0.482 2.972 3570 Z= 0.277 Chirality : 0.050 0.133 468 Planarity : 0.002 0.009 444 Dihedral : 4.705 14.406 378 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.07 % Allowed : 19.26 % Favored : 76.67 % 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: -2.69 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR B 39 PHE 0.012 0.003 PHE F 94 HIS 0.005 0.003 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 2640) covalent geometry : angle 0.48196 ( 3570) hydrogen bonds : bond 0.02099 ( 30) hydrogen bonds : angle 4.67855 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.063 Fit side-chains REVERT: D 60 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7494 (tttp) REVERT: E 43 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7357 (mptp) REVERT: E 62 GLN cc_start: 0.6911 (tt0) cc_final: 0.6391 (tp40) REVERT: A 62 GLN cc_start: 0.7074 (tt0) cc_final: 0.6702 (tp40) REVERT: F 83 GLU cc_start: 0.7399 (tm-30) cc_final: 0.7089 (tm-30) REVERT: B 57 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8373 (mt-10) REVERT: B 62 GLN cc_start: 0.7312 (tm-30) cc_final: 0.6886 (tm-30) outliers start: 11 outliers final: 7 residues processed: 48 average time/residue: 0.5305 time to fit residues: 25.9555 Evaluate side-chains 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 35 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 = 0.4832 r_free = 0.4832 target = 0.215458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.164672 restraints weight = 2613.667| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 2.70 r_work: 0.4232 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2640 Z= 0.231 Angle : 0.604 3.360 3570 Z= 0.349 Chirality : 0.052 0.129 468 Planarity : 0.002 0.009 444 Dihedral : 5.365 15.617 378 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.21 % Favored : 85.79 % Rotamer: Outliers : 3.70 % Allowed : 19.63 % Favored : 76.67 % 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: -2.74 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR B 39 PHE 0.020 0.005 PHE B 94 HIS 0.007 0.004 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 2640) covalent geometry : angle 0.60430 ( 3570) hydrogen bonds : bond 0.02604 ( 30) hydrogen bonds : angle 4.86073 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.080 Fit side-chains REVERT: C 46 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7736 (pt0) REVERT: C 80 LYS cc_start: 0.8062 (tttm) cc_final: 0.7748 (tttp) REVERT: D 46 GLU cc_start: 0.8100 (pt0) cc_final: 0.7753 (pt0) REVERT: D 60 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7382 (tttt) REVERT: E 43 LYS cc_start: 0.7851 (mtmm) cc_final: 0.7567 (mptp) REVERT: A 62 GLN cc_start: 0.6915 (tt0) cc_final: 0.6412 (tp40) REVERT: F 62 GLN cc_start: 0.6514 (tt0) cc_final: 0.6225 (tp40) REVERT: F 83 GLU cc_start: 0.7272 (tm-30) cc_final: 0.7010 (tm-30) REVERT: B 57 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8091 (mt-10) REVERT: B 62 GLN cc_start: 0.7299 (tm-30) cc_final: 0.6860 (tm-30) outliers start: 10 outliers final: 7 residues processed: 55 average time/residue: 0.5983 time to fit residues: 33.5123 Evaluate side-chains 58 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.221509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.176774 restraints weight = 2683.499| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 2.35 r_work: 0.4259 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.4140 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2640 Z= 0.219 Angle : 0.605 4.360 3570 Z= 0.347 Chirality : 0.052 0.131 468 Planarity : 0.002 0.008 444 Dihedral : 5.237 15.266 378 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.11 % Favored : 86.89 % Rotamer: Outliers : 3.70 % Allowed : 20.00 % Favored : 76.30 % 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: -2.77 (0.39), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR B 39 PHE 0.018 0.005 PHE B 94 HIS 0.007 0.004 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 2640) covalent geometry : angle 0.60456 ( 3570) hydrogen bonds : bond 0.02529 ( 30) hydrogen bonds : angle 4.83706 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.102 Fit side-chains REVERT: C 46 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7816 (pt0) REVERT: C 80 LYS cc_start: 0.8047 (tttm) cc_final: 0.7715 (tttp) REVERT: D 60 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7419 (tttt) REVERT: E 43 LYS cc_start: 0.7902 (mtmm) cc_final: 0.7550 (mptp) REVERT: E 62 GLN cc_start: 0.6879 (tt0) cc_final: 0.6506 (tt0) REVERT: A 62 GLN cc_start: 0.7016 (tt0) cc_final: 0.6519 (tp40) REVERT: F 62 GLN cc_start: 0.6637 (tt0) cc_final: 0.6280 (tp40) REVERT: F 83 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7167 (tm-30) REVERT: B 57 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8336 (mt-10) REVERT: B 62 GLN cc_start: 0.7418 (tm-30) cc_final: 0.6991 (tm-30) outliers start: 10 outliers final: 7 residues processed: 55 average time/residue: 0.6063 time to fit residues: 34.0189 Evaluate side-chains 59 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.4859 r_free = 0.4859 target = 0.218535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.167596 restraints weight = 2657.789| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 2.74 r_work: 0.4263 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2640 Z= 0.157 Angle : 0.543 4.583 3570 Z= 0.309 Chirality : 0.051 0.133 468 Planarity : 0.002 0.009 444 Dihedral : 4.937 14.834 378 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 3.33 % Allowed : 20.37 % Favored : 76.30 % 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: -2.72 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR B 39 PHE 0.014 0.004 PHE B 94 HIS 0.006 0.003 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 2640) covalent geometry : angle 0.54287 ( 3570) hydrogen bonds : bond 0.02250 ( 30) hydrogen bonds : angle 4.76353 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.070 Fit side-chains REVERT: C 46 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7711 (pt0) REVERT: C 80 LYS cc_start: 0.7973 (tttm) cc_final: 0.7715 (tttp) REVERT: D 60 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7320 (tttt) REVERT: E 43 LYS cc_start: 0.7875 (mtmm) cc_final: 0.7591 (mptp) REVERT: E 62 GLN cc_start: 0.6740 (tt0) cc_final: 0.6361 (tt0) REVERT: A 62 GLN cc_start: 0.6992 (tt0) cc_final: 0.6515 (tp40) REVERT: F 62 GLN cc_start: 0.6430 (tt0) cc_final: 0.6115 (tp40) REVERT: F 83 GLU cc_start: 0.7306 (tm-30) cc_final: 0.7035 (tm-30) REVERT: B 57 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8170 (mt-10) REVERT: B 62 GLN cc_start: 0.7254 (tm-30) cc_final: 0.6835 (tm-30) outliers start: 9 outliers final: 7 residues processed: 50 average time/residue: 0.6015 time to fit residues: 30.6856 Evaluate side-chains 55 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 0.0370 chunk 5 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 overall best weight: 3.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN F 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.214813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.163974 restraints weight = 2687.403| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 2.74 r_work: 0.4228 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2640 Z= 0.226 Angle : 0.621 4.646 3570 Z= 0.355 Chirality : 0.052 0.131 468 Planarity : 0.002 0.009 444 Dihedral : 5.369 15.369 378 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.75 % Favored : 85.25 % Rotamer: Outliers : 4.07 % Allowed : 20.37 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.73 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR B 39 PHE 0.019 0.005 PHE B 94 HIS 0.007 0.004 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 2640) covalent geometry : angle 0.62067 ( 3570) hydrogen bonds : bond 0.02493 ( 30) hydrogen bonds : angle 4.85587 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.098 Fit side-chains REVERT: C 46 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7760 (pt0) REVERT: C 80 LYS cc_start: 0.8008 (tttm) cc_final: 0.7679 (tttp) REVERT: D 60 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7381 (tttt) REVERT: E 43 LYS cc_start: 0.7925 (mtmm) cc_final: 0.7670 (mptp) REVERT: A 62 GLN cc_start: 0.6905 (tt0) cc_final: 0.6412 (tp40) REVERT: F 62 GLN cc_start: 0.6425 (tt0) cc_final: 0.6160 (tp40) REVERT: F 83 GLU cc_start: 0.7338 (tm-30) cc_final: 0.7080 (tm-30) REVERT: B 57 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8161 (mt-10) REVERT: B 62 GLN cc_start: 0.7294 (tm-30) cc_final: 0.6854 (tm-30) outliers start: 11 outliers final: 7 residues processed: 53 average time/residue: 0.5526 time to fit residues: 29.9439 Evaluate side-chains 57 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 2 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 = 0.4876 r_free = 0.4876 target = 0.223659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.178818 restraints weight = 2708.664| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 2.39 r_work: 0.4281 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.4160 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2640 Z= 0.166 Angle : 0.567 4.819 3570 Z= 0.321 Chirality : 0.051 0.132 468 Planarity : 0.002 0.008 444 Dihedral : 5.083 15.118 378 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 2.96 % Allowed : 21.48 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.71 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR B 39 PHE 0.014 0.004 PHE F 94 HIS 0.006 0.003 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 2640) covalent geometry : angle 0.56656 ( 3570) hydrogen bonds : bond 0.02250 ( 30) hydrogen bonds : angle 4.81696 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.056 Fit side-chains REVERT: C 46 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7795 (pt0) REVERT: C 80 LYS cc_start: 0.8027 (tttm) cc_final: 0.7664 (tttp) REVERT: D 60 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7377 (tttt) REVERT: E 43 LYS cc_start: 0.7924 (mtmm) cc_final: 0.7665 (mptp) REVERT: E 62 GLN cc_start: 0.6876 (tt0) cc_final: 0.6501 (tt0) REVERT: A 62 GLN cc_start: 0.7174 (tt0) cc_final: 0.6693 (tp40) REVERT: F 62 GLN cc_start: 0.6577 (tt0) cc_final: 0.6249 (tp40) REVERT: F 83 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7059 (tm-30) REVERT: B 57 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8340 (mt-10) REVERT: B 62 GLN cc_start: 0.7373 (tm-30) cc_final: 0.6958 (tm-30) outliers start: 8 outliers final: 6 residues processed: 49 average time/residue: 0.4575 time to fit residues: 22.8702 Evaluate side-chains 54 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 10 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.4894 r_free = 0.4894 target = 0.224985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.179950 restraints weight = 2685.854| |-----------------------------------------------------------------------------| r_work (start): 0.4431 rms_B_bonded: 2.38 r_work: 0.4322 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4206 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2640 Z= 0.126 Angle : 0.519 4.669 3570 Z= 0.292 Chirality : 0.050 0.132 468 Planarity : 0.002 0.008 444 Dihedral : 4.770 14.558 378 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.96 % Allowed : 21.48 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.65 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR B 39 PHE 0.012 0.003 PHE B 94 HIS 0.005 0.002 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 2640) covalent geometry : angle 0.51857 ( 3570) hydrogen bonds : bond 0.01999 ( 30) hydrogen bonds : angle 4.70185 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1200.55 seconds wall clock time: 21 minutes 13.27 seconds (1273.27 seconds total)