Starting phenix.real_space_refine on Mon Feb 10 21:02:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xo2_33334/02_2025/7xo2_33334.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xo2_33334/02_2025/7xo2_33334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xo2_33334/02_2025/7xo2_33334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xo2_33334/02_2025/7xo2_33334.map" model { file = "/net/cci-nas-00/data/ceres_data/7xo2_33334/02_2025/7xo2_33334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xo2_33334/02_2025/7xo2_33334.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 1602 2.51 5 N 444 2.21 5 O 504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2550 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Restraints were copied for chains: C, B, E, D, I Time building chain proxies: 1.71, per 1000 atoms: 0.67 Number of scatterers: 2550 At special positions: 0 Unit cell: (96.46, 94.34, 33.92, 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 504 8.00 N 444 7.00 C 1602 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: 0.55 Conformation dependent library (CDL) restraints added in 325.0 milliseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 56.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'I' and resid 37 through 45 removed outlier: 6.598A pdb=" N VAL D 37 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL E 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR D 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N SER E 42 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY D 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N THR E 44 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LYS D 43 " --> pdb=" O THR E 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 48 through 57 removed outlier: 6.639A pdb=" N VAL I 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLY D 51 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N HIS I 50 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA D 53 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 9.260A pdb=" N VAL I 52 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 10.566A pdb=" N VAL D 55 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N THR I 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 10.271A pdb=" N GLU D 57 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ALA I 56 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL D 49 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N HIS E 50 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLY D 51 " --> pdb=" O HIS E 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 61 through 66 removed outlier: 6.349A pdb=" N GLU I 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR D 64 " --> pdb=" O GLU I 61 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL I 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL D 66 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASN I 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU D 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N THR E 64 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL D 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL E 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASN D 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'I' and resid 69 through 72 Processing sheet with id=AA5, first strand: chain 'I' and resid 75 through 79 Processing sheet with id=AA6, first strand: chain 'I' and resid 82 through 83 removed outlier: 6.488A pdb=" N VAL I 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL D 82 " --> pdb=" O GLU E 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'I' and resid 87 through 88 Processing sheet with id=AA8, first strand: chain 'I' and resid 92 through 96 Processing sheet with id=AA9, first strand: chain 'C' and resid 37 through 45 removed outlier: 6.631A pdb=" N VAL C 37 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL A 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR C 39 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N SER A 42 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY C 41 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N THR A 44 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS C 43 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 37 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL B 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR A 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N SER B 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY A 41 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N THR B 44 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LYS A 43 " --> pdb=" O THR B 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 48 through 57 removed outlier: 6.946A pdb=" N VAL C 49 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N HIS A 50 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLY C 51 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N GLY B 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N HIS A 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA B 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N VAL A 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 10.509A pdb=" N VAL B 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N THR A 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 10.201A pdb=" N GLU B 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N ALA A 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 61 through 66 removed outlier: 6.250A pdb=" N GLU C 61 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N THR A 64 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL C 63 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL A 66 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN C 65 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLU A 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N THR B 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL B 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN A 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 69 through 72 Processing sheet with id=AB4, first strand: chain 'C' and resid 75 through 79 Processing sheet with id=AB5, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.573A pdb=" N VAL C 82 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 82 " --> pdb=" O GLU B 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AB7, first strand: chain 'C' and resid 92 through 96 68 hydrogen bonds defined for protein. 204 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: 0.61 Time building geometry restraints manager: 0.66 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: 438 1.29 - 1.36: 402 1.36 - 1.42: 102 1.42 - 1.48: 420 1.48 - 1.55: 1200 Bond restraints: 2562 Sorted by residual: bond pdb=" CA LYS A 60 " pdb=" C LYS A 60 " ideal model delta sigma weight residual 1.522 1.527 -0.005 9.30e-03 1.16e+04 3.00e-01 bond pdb=" CA LYS D 60 " pdb=" C LYS D 60 " ideal model delta sigma weight residual 1.522 1.527 -0.005 9.30e-03 1.16e+04 2.97e-01 bond pdb=" CA LYS C 60 " pdb=" C LYS C 60 " ideal model delta sigma weight residual 1.522 1.527 -0.005 9.30e-03 1.16e+04 2.72e-01 bond pdb=" CA LYS B 60 " pdb=" C LYS B 60 " ideal model delta sigma weight residual 1.522 1.527 -0.005 9.30e-03 1.16e+04 2.66e-01 bond pdb=" CA LYS E 60 " pdb=" C LYS E 60 " ideal model delta sigma weight residual 1.522 1.527 -0.005 9.30e-03 1.16e+04 2.53e-01 ... (remaining 2557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.44: 2874 0.44 - 0.89: 451 0.89 - 1.33: 104 1.33 - 1.77: 13 1.77 - 2.22: 20 Bond angle restraints: 3462 Sorted by residual: angle pdb=" C THR D 59 " pdb=" N LYS D 60 " pdb=" CA LYS D 60 " ideal model delta sigma weight residual 122.17 120.34 1.83 1.54e+00 4.22e-01 1.42e+00 angle pdb=" C THR C 59 " pdb=" N LYS C 60 " pdb=" CA LYS C 60 " ideal model delta sigma weight residual 122.17 120.35 1.82 1.54e+00 4.22e-01 1.40e+00 angle pdb=" C THR B 59 " pdb=" N LYS B 60 " pdb=" CA LYS B 60 " ideal model delta sigma weight residual 122.17 120.35 1.82 1.54e+00 4.22e-01 1.40e+00 angle pdb=" C THR E 59 " pdb=" N LYS E 60 " pdb=" CA LYS E 60 " ideal model delta sigma weight residual 122.17 120.35 1.82 1.54e+00 4.22e-01 1.39e+00 angle pdb=" C THR A 59 " pdb=" N LYS A 60 " pdb=" CA LYS A 60 " ideal model delta sigma weight residual 122.17 120.37 1.80 1.54e+00 4.22e-01 1.37e+00 ... (remaining 3457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.35: 1296 15.35 - 30.70: 96 30.70 - 46.05: 66 46.05 - 61.40: 24 61.40 - 76.75: 6 Dihedral angle restraints: 1488 sinusoidal: 492 harmonic: 996 Sorted by residual: dihedral pdb=" CA GLU C 83 " pdb=" CB GLU C 83 " pdb=" CG GLU C 83 " pdb=" CD GLU C 83 " ideal model delta sinusoidal sigma weight residual -180.00 -127.38 -52.62 3 1.50e+01 4.44e-03 9.13e+00 dihedral pdb=" CA GLU D 83 " pdb=" CB GLU D 83 " pdb=" CG GLU D 83 " pdb=" CD GLU D 83 " ideal model delta sinusoidal sigma weight residual -180.00 -127.39 -52.61 3 1.50e+01 4.44e-03 9.13e+00 dihedral pdb=" CA GLU E 83 " pdb=" CB GLU E 83 " pdb=" CG GLU E 83 " pdb=" CD GLU E 83 " ideal model delta sinusoidal sigma weight residual -180.00 -127.41 -52.59 3 1.50e+01 4.44e-03 9.13e+00 ... (remaining 1485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 227 0.025 - 0.050: 107 0.050 - 0.075: 38 0.075 - 0.100: 17 0.100 - 0.125: 67 Chirality restraints: 456 Sorted by residual: chirality pdb=" CA ILE E 88 " pdb=" N ILE E 88 " pdb=" C ILE E 88 " pdb=" CB ILE E 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA ILE B 88 " pdb=" N ILE B 88 " pdb=" C ILE B 88 " pdb=" CB ILE B 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 453 not shown) Planarity restraints: 426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 59 " -0.002 2.00e-02 2.50e+03 4.26e-03 1.81e-01 pdb=" C THR E 59 " 0.007 2.00e-02 2.50e+03 pdb=" O THR E 59 " -0.003 2.00e-02 2.50e+03 pdb=" N LYS E 60 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 59 " 0.002 2.00e-02 2.50e+03 4.13e-03 1.70e-01 pdb=" C THR C 59 " -0.007 2.00e-02 2.50e+03 pdb=" O THR C 59 " 0.003 2.00e-02 2.50e+03 pdb=" N LYS C 60 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 59 " -0.002 2.00e-02 2.50e+03 4.00e-03 1.60e-01 pdb=" C THR D 59 " 0.007 2.00e-02 2.50e+03 pdb=" O THR D 59 " -0.003 2.00e-02 2.50e+03 pdb=" N LYS D 60 " -0.002 2.00e-02 2.50e+03 ... (remaining 423 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 1576 3.05 - 3.51: 2243 3.51 - 3.97: 3534 3.97 - 4.44: 3796 4.44 - 4.90: 7142 Nonbonded interactions: 18291 Sorted by model distance: nonbonded pdb=" NE2 GLN E 62 " pdb=" OG1 THR E 64 " model vdw 2.586 3.120 nonbonded pdb=" NE2 GLN A 62 " pdb=" OG1 THR A 64 " model vdw 2.586 3.120 nonbonded pdb=" NE2 GLN I 62 " pdb=" OG1 THR I 64 " model vdw 2.586 3.120 nonbonded pdb=" NE2 GLN B 62 " pdb=" OG1 THR B 64 " model vdw 2.586 3.120 nonbonded pdb=" NE2 GLN C 62 " pdb=" OG1 THR C 64 " model vdw 2.587 3.120 ... (remaining 18286 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.020 Set scattering table: 0.040 Process input model: 10.740 Find NCS groups from input model: 0.060 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:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 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 : 0.001 0.014 2562 Z= 0.101 Angle : 0.376 2.215 3462 Z= 0.225 Chirality : 0.052 0.125 456 Planarity : 0.001 0.004 426 Dihedral : 18.118 76.747 864 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 18.60 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.44), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.67 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS A 50 PHE 0.002 0.000 PHE B 94 TYR 0.006 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.300 Fit side-chains REVERT: E 58 LYS cc_start: 0.8958 (mmtp) cc_final: 0.6762 (pptt) REVERT: B 39 TYR cc_start: 0.8691 (t80) cc_final: 0.8257 (t80) REVERT: B 58 LYS cc_start: 0.8794 (mmtp) cc_final: 0.6507 (pptt) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 1.4439 time to fit residues: 45.8553 Evaluate side-chains 19 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.097142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.086103 restraints weight = 4315.114| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.10 r_work: 0.3283 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2562 Z= 0.333 Angle : 0.483 2.984 3462 Z= 0.283 Chirality : 0.054 0.130 456 Planarity : 0.002 0.006 426 Dihedral : 4.375 15.242 372 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 5.04 % Allowed : 17.05 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.43), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.81 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.011 0.002 PHE I 94 TYR 0.007 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 25 time to evaluate : 0.313 Fit side-chains REVERT: I 60 LYS cc_start: 0.6486 (OUTLIER) cc_final: 0.3975 (tptp) REVERT: E 57 GLU cc_start: 0.8502 (pt0) cc_final: 0.8193 (pt0) REVERT: E 58 LYS cc_start: 0.9213 (mmtp) cc_final: 0.6706 (pptt) REVERT: E 60 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.6352 (pmtt) REVERT: B 58 LYS cc_start: 0.9093 (mmtp) cc_final: 0.6546 (pptt) REVERT: B 60 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.6302 (pmtt) outliers start: 13 outliers final: 4 residues processed: 37 average time/residue: 1.7218 time to fit residues: 64.8869 Evaluate side-chains 30 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain B residue 60 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.096218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.085403 restraints weight = 4321.538| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.07 r_work: 0.3267 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2562 Z= 0.295 Angle : 0.464 2.900 3462 Z= 0.272 Chirality : 0.054 0.134 456 Planarity : 0.002 0.008 426 Dihedral : 4.644 15.837 372 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.65 % Allowed : 17.44 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.43), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.99 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.009 0.002 PHE I 94 TYR 0.008 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 23 time to evaluate : 0.256 Fit side-chains REVERT: I 60 LYS cc_start: 0.6583 (OUTLIER) cc_final: 0.6272 (ptpp) REVERT: E 60 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6386 (pmtt) REVERT: B 60 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6305 (pmtt) REVERT: B 80 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.9137 (mtpt) outliers start: 12 outliers final: 5 residues processed: 34 average time/residue: 1.7538 time to fit residues: 60.7437 Evaluate side-chains 29 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 80 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.093273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.082540 restraints weight = 4390.634| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.08 r_work: 0.3223 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 2562 Z= 0.403 Angle : 0.527 3.469 3462 Z= 0.306 Chirality : 0.055 0.138 456 Planarity : 0.002 0.007 426 Dihedral : 5.187 18.797 372 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 4.26 % Allowed : 20.54 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.010 0.002 PHE I 94 TYR 0.005 0.001 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.318 Fit side-chains REVERT: E 60 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.6415 (pmtt) REVERT: B 60 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.6277 (pmtt) outliers start: 11 outliers final: 7 residues processed: 34 average time/residue: 2.0024 time to fit residues: 69.2517 Evaluate side-chains 32 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain B residue 60 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 2 optimal weight: 0.3980 chunk 15 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.096073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.085286 restraints weight = 4393.752| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.08 r_work: 0.3266 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2562 Z= 0.274 Angle : 0.460 2.808 3462 Z= 0.270 Chirality : 0.054 0.133 456 Planarity : 0.002 0.007 426 Dihedral : 4.795 17.121 372 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.65 % Allowed : 20.16 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS C 50 PHE 0.008 0.002 PHE I 94 TYR 0.005 0.001 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 21 time to evaluate : 0.276 Fit side-chains REVERT: I 60 LYS cc_start: 0.6562 (OUTLIER) cc_final: 0.6259 (ptpp) REVERT: E 60 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.6405 (pmtt) REVERT: B 60 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.6251 (pmtt) outliers start: 12 outliers final: 6 residues processed: 31 average time/residue: 1.8526 time to fit residues: 58.5242 Evaluate side-chains 28 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 80 LYS Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain B residue 60 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 0 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.100995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.090136 restraints weight = 4389.060| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.23 r_work: 0.3344 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2562 Z= 0.143 Angle : 0.382 2.396 3462 Z= 0.225 Chirality : 0.053 0.131 456 Planarity : 0.001 0.006 426 Dihedral : 4.198 15.060 372 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.49 % Allowed : 22.09 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.006 0.001 PHE I 94 TYR 0.008 0.001 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.289 Fit side-chains REVERT: E 60 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.6462 (pmtt) REVERT: B 60 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6262 (pmtt) REVERT: B 87 SER cc_start: 0.8875 (p) cc_final: 0.8641 (t) outliers start: 9 outliers final: 2 residues processed: 30 average time/residue: 1.6002 time to fit residues: 49.0220 Evaluate side-chains 27 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain B residue 60 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.092081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.081535 restraints weight = 4484.826| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.07 r_work: 0.3203 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 2562 Z= 0.501 Angle : 0.569 3.822 3462 Z= 0.329 Chirality : 0.057 0.146 456 Planarity : 0.002 0.007 426 Dihedral : 5.499 20.640 372 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 3.49 % Allowed : 22.48 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 50 PHE 0.011 0.002 PHE I 94 TYR 0.011 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.309 Fit side-chains REVERT: E 60 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.6417 (pmtt) REVERT: B 60 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.6306 (pmtt) outliers start: 9 outliers final: 6 residues processed: 32 average time/residue: 1.9675 time to fit residues: 64.1000 Evaluate side-chains 30 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain B residue 60 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 2 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.097312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.086643 restraints weight = 4383.050| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.19 r_work: 0.3289 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2562 Z= 0.214 Angle : 0.437 2.680 3462 Z= 0.257 Chirality : 0.053 0.135 456 Planarity : 0.001 0.006 426 Dihedral : 4.722 16.912 372 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.49 % Allowed : 23.64 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS C 50 PHE 0.007 0.002 PHE A 94 TYR 0.012 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.294 Fit side-chains REVERT: E 60 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.6394 (pmtt) REVERT: B 60 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.6172 (pmtt) REVERT: B 87 SER cc_start: 0.8972 (p) cc_final: 0.8608 (t) outliers start: 9 outliers final: 5 residues processed: 29 average time/residue: 1.6374 time to fit residues: 48.4950 Evaluate side-chains 28 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain B residue 60 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.095901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.085602 restraints weight = 4304.817| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.08 r_work: 0.3269 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2562 Z= 0.272 Angle : 0.454 2.733 3462 Z= 0.265 Chirality : 0.054 0.132 456 Planarity : 0.002 0.006 426 Dihedral : 4.834 16.847 372 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.10 % Allowed : 24.03 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS C 50 PHE 0.008 0.002 PHE C 94 TYR 0.009 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.290 Fit side-chains REVERT: E 60 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.6402 (pmtt) REVERT: B 60 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.6274 (pmtt) REVERT: B 87 SER cc_start: 0.9009 (p) cc_final: 0.8653 (t) outliers start: 8 outliers final: 6 residues processed: 29 average time/residue: 1.6286 time to fit residues: 48.2852 Evaluate side-chains 29 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain B residue 60 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.092927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.082341 restraints weight = 4405.491| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.05 r_work: 0.3218 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 2562 Z= 0.433 Angle : 0.548 3.486 3462 Z= 0.319 Chirality : 0.056 0.136 456 Planarity : 0.002 0.007 426 Dihedral : 5.351 19.389 372 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.10 % Allowed : 24.03 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS C 50 PHE 0.010 0.002 PHE I 94 TYR 0.009 0.002 TYR B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.300 Fit side-chains REVERT: E 60 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.6425 (pmtt) REVERT: B 60 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.6293 (pmtt) outliers start: 8 outliers final: 6 residues processed: 29 average time/residue: 1.8004 time to fit residues: 53.2461 Evaluate side-chains 30 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain B residue 60 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 4 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.098797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.088084 restraints weight = 4402.261| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.21 r_work: 0.3313 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2562 Z= 0.168 Angle : 0.414 2.562 3462 Z= 0.244 Chirality : 0.053 0.133 456 Planarity : 0.001 0.006 426 Dihedral : 4.584 16.370 372 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.10 % Allowed : 24.03 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.006 0.001 PHE I 94 TYR 0.010 0.001 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1938.15 seconds wall clock time: 35 minutes 3.56 seconds (2103.56 seconds total)