Starting phenix.real_space_refine on Wed Sep 17 03:11:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xo0_33332/09_2025/7xo0_33332.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xo0_33332/09_2025/7xo0_33332.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 { model { file = "/net/cci-nas-00/data/ceres_data/7xo0_33332/09_2025/7xo0_33332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xo0_33332/09_2025/7xo0_33332.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xo0_33332/09_2025/7xo0_33332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xo0_33332/09_2025/7xo0_33332.map" } resolution = 3.0 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= 0.004 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 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2550 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "B" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "C" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "E" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "D" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "F" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Time building chain proxies: 0.82, per 1000 atoms: 0.32 Number of scatterers: 2550 At special positions: 0 Unit cell: (92.22, 91.16, 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: 0.18 Conformation dependent library (CDL) restraints added in 113.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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, 43.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 37 through 43 removed outlier: 6.605A pdb=" N VAL A 37 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL D 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR A 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N SER D 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY A 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 48 through 55 removed outlier: 6.934A pdb=" N VAL C 52 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA A 53 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR C 54 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A 55 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLY D 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N HIS A 50 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA D 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N VAL A 52 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 10.592A pdb=" N VAL D 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 9.221A pdb=" N THR A 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 61 through 68 removed outlier: 6.156A pdb=" N GLU A 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N THR D 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL A 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL D 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASN A 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLY D 68 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N GLY A 67 " --> pdb=" O GLY D 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 71 through 72 removed outlier: 6.310A pdb=" N VAL A 71 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 79 removed outlier: 6.641A pdb=" N VAL A 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.598A pdb=" N VAL A 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.417A pdb=" N ILE A 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 95 through 96 removed outlier: 6.512A pdb=" N VAL A 95 " --> pdb=" O LYS C 96 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 37 through 43 removed outlier: 6.589A pdb=" N VAL B 37 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL F 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TYR B 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N SER F 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLY B 41 " --> pdb=" O SER F 42 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 48 through 55 removed outlier: 6.940A pdb=" N VAL E 52 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA B 53 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR E 54 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL B 55 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY F 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N HIS B 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA F 53 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N VAL B 52 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 10.570A pdb=" N VAL F 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N THR B 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 61 through 68 removed outlier: 6.157A pdb=" N GLU B 61 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N THR F 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL B 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL F 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASN B 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N GLY F 68 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLY B 67 " --> pdb=" O GLY F 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 71 through 72 removed outlier: 6.306A pdb=" N VAL B 71 " --> pdb=" O THR F 72 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 77 through 79 removed outlier: 6.651A pdb=" N VAL B 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 82 through 83 removed outlier: 6.628A pdb=" N VAL B 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 87 through 89 removed outlier: 6.425A pdb=" N ILE B 88 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.541A pdb=" N VAL B 95 " --> pdb=" O LYS E 96 " (cutoff:3.500A) 46 hydrogen bonds defined for protein. 138 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: 0.36 Time building geometry restraints manager: 0.26 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 - 1.35: 402 1.35 - 1.42: 102 1.42 - 1.48: 420 1.48 - 1.55: 1200 Bond restraints: 2562 Sorted by residual: bond pdb=" CA VAL F 70 " pdb=" CB VAL F 70 " ideal model delta sigma weight residual 1.533 1.540 -0.008 1.20e-02 6.94e+03 3.97e-01 bond pdb=" CA VAL D 70 " pdb=" CB VAL D 70 " ideal model delta sigma weight residual 1.533 1.540 -0.007 1.20e-02 6.94e+03 3.62e-01 bond pdb=" CA VAL C 70 " pdb=" CB VAL C 70 " ideal model delta sigma weight residual 1.533 1.539 -0.007 1.20e-02 6.94e+03 3.03e-01 bond pdb=" CA LYS E 43 " pdb=" C LYS E 43 " ideal model delta sigma weight residual 1.526 1.531 -0.006 1.08e-02 8.57e+03 2.80e-01 bond pdb=" CA VAL A 70 " pdb=" CB VAL A 70 " ideal model delta sigma weight residual 1.533 1.539 -0.006 1.20e-02 6.94e+03 2.71e-01 ... (remaining 2557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.45: 2818 0.45 - 0.89: 480 0.89 - 1.34: 128 1.34 - 1.79: 24 1.79 - 2.23: 12 Bond angle restraints: 3462 Sorted by residual: angle pdb=" N VAL C 74 " pdb=" CA VAL C 74 " pdb=" C VAL C 74 " ideal model delta sigma weight residual 112.35 110.49 1.86 1.41e+00 5.03e-01 1.74e+00 angle pdb=" N VAL F 74 " pdb=" CA VAL F 74 " pdb=" C VAL F 74 " ideal model delta sigma weight residual 112.35 110.51 1.84 1.41e+00 5.03e-01 1.71e+00 angle pdb=" N VAL D 74 " pdb=" CA VAL D 74 " pdb=" C VAL D 74 " ideal model delta sigma weight residual 112.35 110.51 1.84 1.41e+00 5.03e-01 1.70e+00 angle pdb=" N VAL A 74 " pdb=" CA VAL A 74 " pdb=" C VAL A 74 " ideal model delta sigma weight residual 112.35 110.51 1.84 1.41e+00 5.03e-01 1.70e+00 angle pdb=" N VAL E 74 " pdb=" CA VAL E 74 " pdb=" C VAL E 74 " ideal model delta sigma weight residual 112.35 110.51 1.84 1.41e+00 5.03e-01 1.70e+00 ... (remaining 3457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.00: 1260 12.00 - 23.99: 108 23.99 - 35.98: 66 35.98 - 47.98: 18 47.98 - 59.97: 36 Dihedral angle restraints: 1488 sinusoidal: 492 harmonic: 996 Sorted by residual: dihedral pdb=" CG LYS F 58 " pdb=" CD LYS F 58 " pdb=" CE LYS F 58 " pdb=" NZ LYS F 58 " ideal model delta sinusoidal sigma weight residual 180.00 122.87 57.13 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CG LYS B 58 " pdb=" CD LYS B 58 " pdb=" CE LYS B 58 " pdb=" NZ LYS B 58 " ideal model delta sinusoidal sigma weight residual 180.00 122.87 57.13 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CG LYS D 58 " pdb=" CD LYS D 58 " pdb=" CE LYS D 58 " pdb=" NZ LYS D 58 " ideal model delta sinusoidal sigma weight residual 180.00 122.88 57.12 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 1485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 236 0.025 - 0.050: 126 0.050 - 0.075: 12 0.075 - 0.100: 21 0.100 - 0.124: 61 Chirality restraints: 456 Sorted by residual: chirality pdb=" CA ILE D 88 " pdb=" N ILE D 88 " pdb=" C ILE D 88 " pdb=" CB ILE D 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-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 3.81e-01 chirality pdb=" CA ILE C 88 " pdb=" N ILE C 88 " pdb=" C ILE C 88 " pdb=" CB ILE C 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 453 not shown) Planarity restraints: 426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 73 " 0.002 2.00e-02 2.50e+03 4.16e-03 1.73e-01 pdb=" C GLY C 73 " -0.007 2.00e-02 2.50e+03 pdb=" O GLY C 73 " 0.003 2.00e-02 2.50e+03 pdb=" N VAL C 74 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 73 " 0.002 2.00e-02 2.50e+03 4.12e-03 1.70e-01 pdb=" C GLY D 73 " -0.007 2.00e-02 2.50e+03 pdb=" O GLY D 73 " 0.003 2.00e-02 2.50e+03 pdb=" N VAL D 74 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 73 " -0.002 2.00e-02 2.50e+03 4.11e-03 1.69e-01 pdb=" C GLY E 73 " 0.007 2.00e-02 2.50e+03 pdb=" O GLY E 73 " -0.003 2.00e-02 2.50e+03 pdb=" N VAL E 74 " -0.002 2.00e-02 2.50e+03 ... (remaining 423 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 536 2.80 - 3.33: 1921 3.33 - 3.85: 4042 3.85 - 4.38: 4053 4.38 - 4.90: 8187 Nonbonded interactions: 18739 Sorted by model distance: nonbonded pdb=" ND2 ASN A 65 " pdb=" OG1 THR C 92 " model vdw 2.280 3.120 nonbonded pdb=" OG1 THR A 92 " pdb=" ND2 ASN D 65 " model vdw 2.283 3.120 nonbonded pdb=" OG1 THR B 92 " pdb=" ND2 ASN F 65 " model vdw 2.283 3.120 nonbonded pdb=" ND2 ASN B 65 " pdb=" OG1 THR E 92 " model vdw 2.292 3.120 nonbonded pdb=" O ALA A 90 " pdb=" ND2 ASN D 65 " model vdw 2.301 3.120 ... (remaining 18734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 2.060 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: 0.010 Set scattering table: 0.000 Process input model: 4.450 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 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 0.010 2562 Z= 0.100 Angle : 0.392 2.232 3462 Z= 0.243 Chirality : 0.050 0.124 456 Planarity : 0.001 0.004 426 Dihedral : 16.618 59.972 864 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % 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: -2.66 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR E 39 PHE 0.001 0.000 PHE E 94 HIS 0.001 0.000 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00148 ( 2562) covalent geometry : angle 0.39224 ( 3462) hydrogen bonds : bond 0.15290 ( 46) hydrogen bonds : angle 8.30806 ( 138) *********************** 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 19 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.089 Fit side-chains revert: symmetry clash REVERT: D 58 LYS cc_start: 0.8584 (mttt) cc_final: 0.8380 (mttm) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.7410 time to fit residues: 14.4266 Evaluate side-chains 15 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.094 ------------------------------------------------------------------------------- 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: 0.0370 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- 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 = 0.3305 r_free = 0.3305 target = 0.097049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.086201 restraints weight = 3342.878| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.71 r_work: 0.2965 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 2562 Z= 0.222 Angle : 0.463 2.810 3462 Z= 0.278 Chirality : 0.054 0.128 456 Planarity : 0.002 0.007 426 Dihedral : 4.083 13.860 372 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 5.04 % Allowed : 10.47 % Favored : 84.50 % 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: -2.89 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR D 39 PHE 0.004 0.001 PHE C 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 2562) covalent geometry : angle 0.46333 ( 3462) hydrogen bonds : bond 0.02288 ( 46) hydrogen bonds : angle 6.72933 ( 138) *********************** 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 44 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 97 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7605 (mppt) REVERT: E 43 LYS cc_start: 0.8530 (tttt) cc_final: 0.7903 (ttmt) outliers start: 13 outliers final: 5 residues processed: 37 average time/residue: 0.5923 time to fit residues: 22.3675 Evaluate side-chains 34 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.099967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.089236 restraints weight = 3367.001| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.64 r_work: 0.3007 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2562 Z= 0.187 Angle : 0.436 2.567 3462 Z= 0.265 Chirality : 0.054 0.125 456 Planarity : 0.002 0.008 426 Dihedral : 4.057 13.983 372 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.88 % Allowed : 14.34 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.95 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR B 39 PHE 0.004 0.001 PHE C 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 2562) covalent geometry : angle 0.43646 ( 3462) hydrogen bonds : bond 0.02152 ( 46) hydrogen bonds : angle 6.44594 ( 138) *********************** 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 44 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: B 97 LYS cc_start: 0.7976 (mmmt) cc_final: 0.7272 (tmtt) REVERT: C 97 LYS cc_start: 0.8067 (mmmt) cc_final: 0.7807 (mppt) REVERT: E 43 LYS cc_start: 0.8508 (tttt) cc_final: 0.7881 (ttmt) REVERT: E 96 LYS cc_start: 0.8772 (tttt) cc_final: 0.8494 (tppp) REVERT: D 58 LYS cc_start: 0.8738 (mttp) cc_final: 0.8490 (mttm) REVERT: F 97 LYS cc_start: 0.7767 (mptp) cc_final: 0.7362 (mppt) outliers start: 10 outliers final: 5 residues processed: 40 average time/residue: 0.5075 time to fit residues: 20.8064 Evaluate side-chains 38 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain D residue 54 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.0970 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN F 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.099235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.088505 restraints weight = 3409.816| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.68 r_work: 0.2979 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 2562 Z= 0.220 Angle : 0.461 2.621 3462 Z= 0.278 Chirality : 0.055 0.129 456 Planarity : 0.002 0.011 426 Dihedral : 4.181 14.589 372 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 5.04 % Allowed : 14.34 % Favored : 80.62 % 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: -2.95 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR D 39 PHE 0.004 0.001 PHE C 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 2562) covalent geometry : angle 0.46053 ( 3462) hydrogen bonds : bond 0.02170 ( 46) hydrogen bonds : angle 6.35889 ( 138) *********************** 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 47 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.055 Fit side-chains revert: symmetry clash REVERT: B 97 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7408 (tmtt) REVERT: C 97 LYS cc_start: 0.8147 (mmmt) cc_final: 0.7919 (mppt) REVERT: E 43 LYS cc_start: 0.8462 (tttt) cc_final: 0.7813 (ttmt) REVERT: E 96 LYS cc_start: 0.8789 (tttt) cc_final: 0.8495 (tppp) REVERT: F 97 LYS cc_start: 0.7641 (mptp) cc_final: 0.7276 (mppt) outliers start: 13 outliers final: 5 residues processed: 42 average time/residue: 0.4672 time to fit residues: 20.0248 Evaluate side-chains 40 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.101533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.090771 restraints weight = 3293.598| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.66 r_work: 0.3048 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2562 Z= 0.124 Angle : 0.389 2.421 3462 Z= 0.238 Chirality : 0.053 0.126 456 Planarity : 0.001 0.011 426 Dihedral : 3.954 12.615 372 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.16 % Allowed : 18.99 % Favored : 79.84 % 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: -2.76 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR B 39 PHE 0.002 0.001 PHE A 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 2562) covalent geometry : angle 0.38885 ( 3462) hydrogen bonds : bond 0.01685 ( 46) hydrogen bonds : angle 6.09783 ( 138) *********************** 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 37 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.068 Fit side-chains revert: symmetry clash REVERT: B 97 LYS cc_start: 0.8098 (mmmt) cc_final: 0.7533 (tmtt) REVERT: C 97 LYS cc_start: 0.8163 (mmmt) cc_final: 0.7945 (mppt) REVERT: E 43 LYS cc_start: 0.8429 (tttt) cc_final: 0.7827 (ttmt) REVERT: E 96 LYS cc_start: 0.8804 (tttt) cc_final: 0.8531 (tppp) REVERT: F 97 LYS cc_start: 0.7712 (mptp) cc_final: 0.7350 (mppt) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 0.5503 time to fit residues: 20.2673 Evaluate side-chains 37 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.097283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.086671 restraints weight = 3507.557| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.64 r_work: 0.2956 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.033 2562 Z= 0.349 Angle : 0.556 2.683 3462 Z= 0.332 Chirality : 0.058 0.134 456 Planarity : 0.003 0.015 426 Dihedral : 4.479 14.983 372 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 4.26 % Allowed : 16.67 % Favored : 79.07 % 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: -3.02 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR D 39 PHE 0.006 0.002 PHE C 94 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00795 ( 2562) covalent geometry : angle 0.55571 ( 3462) hydrogen bonds : bond 0.02648 ( 46) hydrogen bonds : angle 6.48895 ( 138) *********************** 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 50 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: A 46 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7657 (tt0) REVERT: B 97 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7500 (tmtt) REVERT: C 97 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7944 (mppt) REVERT: E 43 LYS cc_start: 0.8508 (tttt) cc_final: 0.7932 (ttmt) REVERT: E 96 LYS cc_start: 0.8811 (tttt) cc_final: 0.8516 (tppp) REVERT: F 97 LYS cc_start: 0.7696 (mptp) cc_final: 0.7330 (mppt) outliers start: 11 outliers final: 5 residues processed: 44 average time/residue: 0.6576 time to fit residues: 29.4997 Evaluate side-chains 46 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.089205 restraints weight = 3327.092| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.62 r_work: 0.3124 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2562 Z= 0.193 Angle : 0.447 2.536 3462 Z= 0.270 Chirality : 0.054 0.129 456 Planarity : 0.002 0.013 426 Dihedral : 4.247 14.043 372 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 2.71 % Allowed : 19.77 % Favored : 77.52 % 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: -2.94 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR D 39 PHE 0.003 0.001 PHE C 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 2562) covalent geometry : angle 0.44671 ( 3462) hydrogen bonds : bond 0.02013 ( 46) hydrogen bonds : angle 6.23327 ( 138) *********************** 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 42 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 43 LYS cc_start: 0.8473 (tttt) cc_final: 0.7906 (ttmt) REVERT: E 96 LYS cc_start: 0.8817 (tttt) cc_final: 0.8581 (tppp) outliers start: 7 outliers final: 2 residues processed: 39 average time/residue: 0.5917 time to fit residues: 23.5475 Evaluate side-chains 36 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 0.0060 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.102398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.091649 restraints weight = 3334.843| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.65 r_work: 0.3078 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2562 Z= 0.117 Angle : 0.382 2.810 3462 Z= 0.233 Chirality : 0.053 0.128 456 Planarity : 0.001 0.015 426 Dihedral : 3.956 12.662 372 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.16 % Allowed : 20.93 % 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 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 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 39 PHE 0.002 0.001 PHE C 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 2562) covalent geometry : angle 0.38220 ( 3462) hydrogen bonds : bond 0.01604 ( 46) hydrogen bonds : angle 6.00237 ( 138) *********************** 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 38 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.092 Fit side-chains REVERT: A 97 LYS cc_start: 0.8029 (mmmt) cc_final: 0.7780 (mppt) REVERT: B 97 LYS cc_start: 0.8335 (mptp) cc_final: 0.7490 (tmtt) REVERT: E 96 LYS cc_start: 0.8809 (tttt) cc_final: 0.8548 (tppp) REVERT: E 97 LYS cc_start: 0.8256 (mptp) cc_final: 0.7782 (mppt) REVERT: F 97 LYS cc_start: 0.7710 (mptp) cc_final: 0.7375 (mppt) outliers start: 3 outliers final: 2 residues processed: 38 average time/residue: 0.5934 time to fit residues: 23.0806 Evaluate side-chains 36 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 29 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.098659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.087381 restraints weight = 3384.795| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.77 r_work: 0.3131 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2562 Z= 0.109 Angle : 0.376 3.360 3462 Z= 0.229 Chirality : 0.052 0.127 456 Planarity : 0.001 0.016 426 Dihedral : 3.860 12.077 372 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.16 % Allowed : 20.16 % Favored : 78.68 % 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: -2.57 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 39 PHE 0.002 0.001 PHE C 94 HIS 0.001 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 2562) covalent geometry : angle 0.37553 ( 3462) hydrogen bonds : bond 0.01506 ( 46) hydrogen bonds : angle 5.89502 ( 138) *********************** 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 37 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.102 Fit side-chains REVERT: B 97 LYS cc_start: 0.8276 (mptp) cc_final: 0.7401 (tmtt) REVERT: E 96 LYS cc_start: 0.8809 (tttt) cc_final: 0.8547 (tppp) REVERT: E 97 LYS cc_start: 0.8277 (mptp) cc_final: 0.7786 (mppt) REVERT: F 97 LYS cc_start: 0.7779 (mptp) cc_final: 0.7394 (mppt) outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 0.5398 time to fit residues: 20.4924 Evaluate side-chains 36 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.099084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.088850 restraints weight = 3503.915| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.57 r_work: 0.2978 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.043 2562 Z= 0.340 Angle : 0.547 2.697 3462 Z= 0.327 Chirality : 0.058 0.134 456 Planarity : 0.003 0.018 426 Dihedral : 4.485 14.900 372 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 2.33 % Allowed : 19.38 % Favored : 78.29 % 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: -2.91 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR E 39 PHE 0.006 0.002 PHE C 94 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00772 ( 2562) covalent geometry : angle 0.54659 ( 3462) hydrogen bonds : bond 0.02506 ( 46) hydrogen bonds : angle 6.33572 ( 138) ********************** 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 45 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.098 Fit side-chains REVERT: B 97 LYS cc_start: 0.8384 (mptp) cc_final: 0.7471 (tmtt) REVERT: E 96 LYS cc_start: 0.8811 (tttt) cc_final: 0.8540 (tppp) REVERT: E 97 LYS cc_start: 0.8239 (mptp) cc_final: 0.7793 (mppt) REVERT: F 97 LYS cc_start: 0.7764 (mptp) cc_final: 0.7393 (mppt) outliers start: 6 outliers final: 3 residues processed: 44 average time/residue: 0.7221 time to fit residues: 32.3869 Evaluate side-chains 41 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.103130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.092360 restraints weight = 3344.904| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.64 r_work: 0.3105 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 : 0.002 0.014 2562 Z= 0.101 Angle : 0.382 3.603 3462 Z= 0.233 Chirality : 0.053 0.126 456 Planarity : 0.001 0.016 426 Dihedral : 3.965 12.531 372 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.33 % Allowed : 19.38 % Favored : 78.29 % 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 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 39 PHE 0.002 0.000 PHE A 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 2562) covalent geometry : angle 0.38181 ( 3462) hydrogen bonds : bond 0.01513 ( 46) hydrogen bonds : angle 5.88089 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 967.95 seconds wall clock time: 17 minutes 20.86 seconds (1040.86 seconds total)