Starting phenix.real_space_refine on Wed Mar 5 15:58:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xo0_33332/03_2025/7xo0_33332.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xo0_33332/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xo0_33332/03_2025/7xo0_33332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xo0_33332/03_2025/7xo0_33332.map" model { file = "/net/cci-nas-00/data/ceres_data/7xo0_33332/03_2025/7xo0_33332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xo0_33332/03_2025/7xo0_33332.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= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 2.62, per 1000 atoms: 1.03 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: 0.54 Conformation dependent library (CDL) restraints added in 318.3 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, 43.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 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: 0.57 Time building geometry restraints manager: 0.65 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 1.710 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.820 Find NCS groups from input model: 0.060 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:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.860 ------------------------------------------------------------------------------- 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= 0.096 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 (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: -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 HIS 0.001 0.000 HIS E 50 PHE 0.001 0.000 PHE E 94 TYR 0.003 0.001 TYR E 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 19 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.291 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: 1.5590 time to fit residues: 30.4492 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 : 0.270 ------------------------------------------------------------------------------- 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: 0.0060 chunk 27 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- 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 = 0.3352 r_free = 0.3352 target = 0.101127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.090666 restraints weight = 3326.359| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.61 r_work: 0.3017 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2562 Z= 0.230 Angle : 0.413 2.729 3462 Z= 0.249 Chirality : 0.053 0.125 456 Planarity : 0.002 0.006 426 Dihedral : 3.886 12.570 372 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.33 % Allowed : 13.18 % 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 (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: -2.73 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.002 0.001 PHE A 94 TYR 0.006 0.001 TYR B 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 37 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: C 97 LYS cc_start: 0.7769 (mmmt) cc_final: 0.7553 (mppt) REVERT: E 43 LYS cc_start: 0.8535 (tttt) cc_final: 0.7941 (ttmt) outliers start: 6 outliers final: 2 residues processed: 36 average time/residue: 1.4169 time to fit residues: 52.1820 Evaluate side-chains 32 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain D residue 54 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3352 r_free = 0.3352 target = 0.100406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.089257 restraints weight = 3310.825| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.73 r_work: 0.3105 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2562 Z= 0.198 Angle : 0.392 2.451 3462 Z= 0.239 Chirality : 0.053 0.124 456 Planarity : 0.002 0.010 426 Dihedral : 3.827 12.606 372 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.33 % Allowed : 14.34 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.74 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.003 0.001 PHE C 94 TYR 0.007 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 41 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 46 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: B 97 LYS cc_start: 0.7907 (mmmt) cc_final: 0.7042 (tmtt) REVERT: E 43 LYS cc_start: 0.8547 (tttt) cc_final: 0.7967 (ttmt) REVERT: E 96 LYS cc_start: 0.8752 (tttt) cc_final: 0.8489 (tppp) REVERT: F 97 LYS cc_start: 0.7643 (mptp) cc_final: 0.7306 (mppt) outliers start: 6 outliers final: 3 residues processed: 39 average time/residue: 1.2441 time to fit residues: 49.7566 Evaluate side-chains 36 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3294 r_free = 0.3294 target = 0.096030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.085324 restraints weight = 3451.401| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.70 r_work: 0.2936 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.038 2562 Z= 0.651 Angle : 0.613 2.792 3462 Z= 0.366 Chirality : 0.061 0.135 456 Planarity : 0.003 0.012 426 Dihedral : 4.545 15.486 372 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 4.65 % Allowed : 14.34 % Favored : 81.01 % 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: -3.10 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.007 0.002 PHE C 94 TYR 0.008 0.002 TYR D 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 53 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.280 Fit side-chains REVERT: A 46 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: A 97 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7836 (mppt) REVERT: B 97 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7440 (tmtt) REVERT: E 43 LYS cc_start: 0.8532 (tttt) cc_final: 0.7965 (ttmt) REVERT: E 96 LYS cc_start: 0.8803 (tttt) cc_final: 0.8512 (tppp) REVERT: F 96 LYS cc_start: 0.8870 (tttt) cc_final: 0.8659 (tttt) REVERT: F 97 LYS cc_start: 0.7690 (mptp) cc_final: 0.7315 (mppt) outliers start: 12 outliers final: 4 residues processed: 47 average time/residue: 1.2841 time to fit residues: 61.7222 Evaluate side-chains 46 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 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 17 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3404 r_free = 0.3404 target = 0.103581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.092984 restraints weight = 3336.012| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.65 r_work: 0.3121 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2562 Z= 0.165 Angle : 0.387 2.358 3462 Z= 0.237 Chirality : 0.053 0.126 456 Planarity : 0.001 0.011 426 Dihedral : 3.996 12.923 372 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.71 % Allowed : 17.05 % Favored : 80.23 % 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: -2.80 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.003 0.001 PHE A 94 TYR 0.010 0.002 TYR D 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 40 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.293 Fit side-chains REVERT: A 46 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7515 (tt0) REVERT: A 97 LYS cc_start: 0.7997 (mmmt) cc_final: 0.7742 (mppt) REVERT: B 97 LYS cc_start: 0.8068 (mmmt) cc_final: 0.7509 (tmtt) REVERT: E 43 LYS cc_start: 0.8452 (tttt) cc_final: 0.7887 (ttmt) REVERT: E 96 LYS cc_start: 0.8784 (tttt) cc_final: 0.8542 (tppp) REVERT: F 97 LYS cc_start: 0.7665 (mptp) cc_final: 0.7355 (mppt) outliers start: 7 outliers final: 4 residues processed: 38 average time/residue: 1.2824 time to fit residues: 49.9519 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 : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain B 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.100683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.090061 restraints weight = 3370.124| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.63 r_work: 0.3040 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2562 Z= 0.197 Angle : 0.392 2.417 3462 Z= 0.239 Chirality : 0.053 0.127 456 Planarity : 0.002 0.012 426 Dihedral : 3.942 12.810 372 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.10 % Allowed : 17.05 % 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 (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: -2.70 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.002 0.001 PHE C 94 TYR 0.007 0.001 TYR C 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 43 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.297 Fit side-chains REVERT: A 46 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7528 (tt0) REVERT: B 97 LYS cc_start: 0.8080 (mmmt) cc_final: 0.7529 (tmtt) REVERT: E 43 LYS cc_start: 0.8382 (tttt) cc_final: 0.7772 (ttmt) REVERT: E 96 LYS cc_start: 0.8799 (tttt) cc_final: 0.8521 (tppp) REVERT: D 97 LYS cc_start: 0.7771 (mmmt) cc_final: 0.7486 (mppt) REVERT: F 97 LYS cc_start: 0.7702 (mptp) cc_final: 0.7344 (mppt) outliers start: 8 outliers final: 6 residues processed: 40 average time/residue: 1.2415 time to fit residues: 50.9526 Evaluate side-chains 41 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 42 SER 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 3 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.099636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.088929 restraints weight = 3410.963| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.64 r_work: 0.3099 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1938 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= 0.286 Angle : 0.435 2.526 3462 Z= 0.264 Chirality : 0.054 0.128 456 Planarity : 0.002 0.015 426 Dihedral : 4.120 13.760 372 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.49 % Allowed : 17.05 % Favored : 79.46 % 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: -2.77 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.003 0.001 PHE C 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 43 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.304 Fit side-chains REVERT: A 46 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: B 97 LYS cc_start: 0.8093 (mmmt) cc_final: 0.7577 (tmtt) REVERT: E 43 LYS cc_start: 0.8438 (tttt) cc_final: 0.7869 (ttmt) REVERT: E 96 LYS cc_start: 0.8816 (tttt) cc_final: 0.8544 (tppp) REVERT: D 97 LYS cc_start: 0.7771 (mmmt) cc_final: 0.7564 (mppt) REVERT: F 97 LYS cc_start: 0.7676 (mptp) cc_final: 0.7370 (mppt) outliers start: 9 outliers final: 6 residues processed: 39 average time/residue: 1.2257 time to fit residues: 49.0582 Evaluate side-chains 41 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 42 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.0030 chunk 2 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 overall best weight: 1.7392 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.101215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.090537 restraints weight = 3335.234| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.63 r_work: 0.3073 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2562 Z= 0.199 Angle : 0.394 2.429 3462 Z= 0.240 Chirality : 0.053 0.127 456 Planarity : 0.002 0.012 426 Dihedral : 3.989 12.758 372 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.49 % Allowed : 17.44 % 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 (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: -2.67 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.002 0.001 PHE C 94 TYR 0.011 0.002 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 44 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.300 Fit side-chains REVERT: A 46 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7620 (tt0) REVERT: B 97 LYS cc_start: 0.8104 (mmmt) cc_final: 0.7567 (tmtt) REVERT: E 96 LYS cc_start: 0.8804 (tttt) cc_final: 0.8552 (tppp) REVERT: D 97 LYS cc_start: 0.7722 (mmmt) cc_final: 0.7519 (mppt) REVERT: F 97 LYS cc_start: 0.7757 (mptp) cc_final: 0.7399 (mppt) outliers start: 9 outliers final: 5 residues processed: 40 average time/residue: 1.2336 time to fit residues: 50.6232 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 : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 96 LYS 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 35 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 32 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.1164 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.102926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.092326 restraints weight = 3299.078| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.65 r_work: 0.3118 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2562 Z= 0.134 Angle : 0.365 3.060 3462 Z= 0.223 Chirality : 0.052 0.126 456 Planarity : 0.001 0.015 426 Dihedral : 3.799 11.673 372 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.33 % Allowed : 18.60 % 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 (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: -2.54 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.002 0.000 PHE A 94 TYR 0.007 0.001 TYR C 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 40 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.275 Fit side-chains REVERT: A 46 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7488 (tt0) REVERT: B 97 LYS cc_start: 0.8126 (mmmt) cc_final: 0.7607 (tmtt) REVERT: E 96 LYS cc_start: 0.8807 (tttt) cc_final: 0.8555 (tppp) REVERT: D 97 LYS cc_start: 0.7766 (mmmt) cc_final: 0.7530 (mppt) REVERT: F 97 LYS cc_start: 0.7757 (mptp) cc_final: 0.7382 (mppt) outliers start: 6 outliers final: 3 residues processed: 39 average time/residue: 1.0901 time to fit residues: 43.7080 Evaluate side-chains 36 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 42 SER 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 13 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 = 0.3364 r_free = 0.3364 target = 0.100023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.089354 restraints weight = 3377.988| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.64 r_work: 0.3038 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2562 Z= 0.239 Angle : 0.411 3.269 3462 Z= 0.250 Chirality : 0.053 0.128 456 Planarity : 0.002 0.016 426 Dihedral : 4.024 13.085 372 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.33 % Allowed : 18.22 % Favored : 79.46 % 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: -2.61 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.002 0.001 PHE C 94 TYR 0.007 0.001 TYR C 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 40 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.270 Fit side-chains REVERT: A 46 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7562 (tt0) REVERT: B 97 LYS cc_start: 0.8106 (mmmt) cc_final: 0.7578 (tmtt) REVERT: E 96 LYS cc_start: 0.8802 (tttt) cc_final: 0.8550 (tppp) REVERT: D 97 LYS cc_start: 0.7687 (mmmt) cc_final: 0.7440 (mppt) REVERT: F 97 LYS cc_start: 0.7817 (mptp) cc_final: 0.7398 (mppt) outliers start: 6 outliers final: 4 residues processed: 38 average time/residue: 1.2453 time to fit residues: 48.5563 Evaluate side-chains 39 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 42 SER 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 4 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 27 optimal weight: 0.0170 chunk 26 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 31 optimal weight: 0.0070 chunk 35 optimal weight: 3.9990 overall best weight: 1.1838 ------------------------------------------------------------------------------- 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 = 0.3404 r_free = 0.3404 target = 0.102853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.092195 restraints weight = 3352.238| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.64 r_work: 0.3082 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2562 Z= 0.143 Angle : 0.370 3.262 3462 Z= 0.226 Chirality : 0.052 0.126 456 Planarity : 0.001 0.015 426 Dihedral : 3.827 11.719 372 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.94 % Allowed : 18.99 % 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 (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: -2.48 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.002 0.000 PHE A 94 TYR 0.012 0.002 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2017.69 seconds wall clock time: 35 minutes 13.74 seconds (2113.74 seconds total)