Starting phenix.real_space_refine on Sat Apr 26 17:32:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lon_63250/04_2025/9lon_63250.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lon_63250/04_2025/9lon_63250.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/9lon_63250/04_2025/9lon_63250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lon_63250/04_2025/9lon_63250.map" model { file = "/net/cci-nas-00/data/ceres_data/9lon_63250/04_2025/9lon_63250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lon_63250/04_2025/9lon_63250.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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1728 2.51 5 N 480 2.21 5 O 564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 2772 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 462 Classifications: {'peptide': 66} Link IDs: {'TRANS': 65} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 2.84, per 1000 atoms: 1.02 Number of scatterers: 2772 At special positions: 0 Unit cell: (75.53, 125.33, 32.37, 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 564 8.00 N 480 7.00 C 1728 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: 0.63 Conformation dependent library (CDL) restraints added in 347.0 milliseconds 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 672 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 42.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 36 through 41 removed outlier: 6.553A pdb=" N GLY A 36 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N TYR D 39 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU A 38 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N GLY D 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A 40 " --> pdb=" O GLY D 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 57 removed outlier: 6.771A pdb=" N VAL A 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR C 53 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR A 54 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL C 55 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA A 56 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLU C 57 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLY A 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N HIS D 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL A 49 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N VAL D 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLY A 51 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N THR D 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N THR A 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 10.377A pdb=" N ALA D 56 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N VAL A 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 61 through 63 removed outlier: 6.374A pdb=" N GLN A 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 70 through 72 removed outlier: 6.411A pdb=" N VAL A 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 75 through 82 removed outlier: 6.543A pdb=" N ALA A 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N GLN C 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA A 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N THR C 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS A 80 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 88 through 89 removed outlier: 6.895A pdb=" N ILE A 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 95 through 96 removed outlier: 6.791A pdb=" N VAL A 95 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 36 through 41 removed outlier: 6.560A pdb=" N GLY B 36 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N TYR F 39 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU B 38 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLY F 41 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 40 " --> pdb=" O GLY F 41 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 47 through 57 removed outlier: 6.762A pdb=" N VAL B 52 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR E 53 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR B 54 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL E 55 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA B 56 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLU E 57 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLY B 47 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N HIS F 50 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 49 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N VAL F 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N GLY B 51 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N THR F 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N THR B 53 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 10.391A pdb=" N ALA F 56 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N VAL B 55 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 61 through 63 removed outlier: 6.370A pdb=" N GLN B 62 " --> pdb=" O VAL F 63 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 70 through 72 removed outlier: 6.403A pdb=" N VAL B 71 " --> pdb=" O THR E 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 75 through 82 removed outlier: 6.542A pdb=" N ALA B 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N GLN E 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA B 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N THR E 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYS B 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 88 through 89 removed outlier: 6.906A pdb=" N ILE B 88 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.809A pdb=" N VAL B 95 " --> pdb=" O LYS F 96 " (cutoff:3.500A) 44 hydrogen bonds defined for protein. 132 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: 0.74 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 492 1.28 - 1.35: 426 1.35 - 1.41: 102 1.41 - 1.48: 462 1.48 - 1.54: 1302 Bond restraints: 2784 Sorted by residual: bond pdb=" CB ASN A 65 " pdb=" CG ASN A 65 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.51e+00 bond pdb=" CB ASN C 65 " pdb=" CG ASN C 65 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.51e+00 bond pdb=" CB ASN E 65 " pdb=" CG ASN E 65 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.46e+00 bond pdb=" CB ASN F 65 " pdb=" CG ASN F 65 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.46e+00 bond pdb=" CB ASN D 65 " pdb=" CG ASN D 65 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.46e+00 ... (remaining 2779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 3441 1.05 - 2.10: 297 2.10 - 3.15: 12 3.15 - 4.20: 6 4.20 - 5.25: 6 Bond angle restraints: 3762 Sorted by residual: angle pdb=" CB LYS B 34 " pdb=" CG LYS B 34 " pdb=" CD LYS B 34 " ideal model delta sigma weight residual 111.30 106.05 5.25 2.30e+00 1.89e-01 5.21e+00 angle pdb=" CB LYS F 34 " pdb=" CG LYS F 34 " pdb=" CD LYS F 34 " ideal model delta sigma weight residual 111.30 106.07 5.23 2.30e+00 1.89e-01 5.18e+00 angle pdb=" CB LYS D 34 " pdb=" CG LYS D 34 " pdb=" CD LYS D 34 " ideal model delta sigma weight residual 111.30 106.08 5.22 2.30e+00 1.89e-01 5.15e+00 angle pdb=" CB LYS C 34 " pdb=" CG LYS C 34 " pdb=" CD LYS C 34 " ideal model delta sigma weight residual 111.30 106.08 5.22 2.30e+00 1.89e-01 5.15e+00 angle pdb=" CB LYS E 34 " pdb=" CG LYS E 34 " pdb=" CD LYS E 34 " ideal model delta sigma weight residual 111.30 106.10 5.20 2.30e+00 1.89e-01 5.12e+00 ... (remaining 3757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.40: 1470 14.40 - 28.80: 114 28.80 - 43.20: 36 43.20 - 57.60: 6 57.60 - 72.00: 6 Dihedral angle restraints: 1632 sinusoidal: 564 harmonic: 1068 Sorted by residual: dihedral pdb=" CG LYS D 34 " pdb=" CD LYS D 34 " pdb=" CE LYS D 34 " pdb=" NZ LYS D 34 " ideal model delta sinusoidal sigma weight residual 180.00 127.01 52.99 3 1.50e+01 4.44e-03 9.17e+00 dihedral pdb=" CG LYS E 34 " pdb=" CD LYS E 34 " pdb=" CE LYS E 34 " pdb=" NZ LYS E 34 " ideal model delta sinusoidal sigma weight residual 180.00 127.02 52.98 3 1.50e+01 4.44e-03 9.17e+00 dihedral pdb=" CG LYS C 34 " pdb=" CD LYS C 34 " pdb=" CE LYS C 34 " pdb=" NZ LYS C 34 " ideal model delta sinusoidal sigma weight residual 180.00 127.04 52.96 3 1.50e+01 4.44e-03 9.16e+00 ... (remaining 1629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 183 0.023 - 0.046: 144 0.046 - 0.069: 75 0.069 - 0.092: 33 0.092 - 0.115: 57 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA VAL C 48 " pdb=" N VAL C 48 " pdb=" C VAL C 48 " pdb=" CB VAL C 48 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.32e-01 chirality pdb=" CA VAL D 77 " pdb=" N VAL D 77 " pdb=" C VAL D 77 " pdb=" CB VAL D 77 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.29e-01 chirality pdb=" CA VAL B 77 " pdb=" N VAL B 77 " pdb=" C VAL B 77 " pdb=" CB VAL B 77 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.29e-01 ... (remaining 489 not shown) Planarity restraints: 468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 94 " -0.010 2.00e-02 2.50e+03 9.22e-03 1.49e+00 pdb=" CG PHE A 94 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE A 94 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 94 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 94 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 94 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 94 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 94 " -0.010 2.00e-02 2.50e+03 9.15e-03 1.47e+00 pdb=" CG PHE C 94 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE C 94 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE C 94 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 94 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 94 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 94 " 0.010 2.00e-02 2.50e+03 9.12e-03 1.46e+00 pdb=" CG PHE E 94 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE E 94 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE E 94 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE E 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE E 94 " 0.002 2.00e-02 2.50e+03 ... (remaining 465 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 932 2.87 - 3.38: 2180 3.38 - 3.88: 4244 3.88 - 4.39: 4330 4.39 - 4.90: 9343 Nonbonded interactions: 21029 Sorted by model distance: nonbonded pdb=" O GLU D 83 " pdb=" ND2 ASN D 87 " model vdw 2.359 3.120 nonbonded pdb=" O GLU B 83 " pdb=" ND2 ASN B 87 " model vdw 2.359 3.120 nonbonded pdb=" O GLU A 83 " pdb=" ND2 ASN A 87 " model vdw 2.360 3.120 nonbonded pdb=" O GLU C 83 " pdb=" ND2 ASN C 87 " model vdw 2.360 3.120 nonbonded pdb=" O GLU F 83 " pdb=" ND2 ASN F 87 " model vdw 2.360 3.120 ... (remaining 21024 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain '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: 2.330 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.840 Find NCS groups from input model: 0.070 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:15.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 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 : 0.009 0.038 2784 Z= 0.417 Angle : 0.651 5.249 3762 Z= 0.397 Chirality : 0.051 0.115 492 Planarity : 0.002 0.011 468 Dihedral : 13.105 72.005 960 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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: -3.50 (0.30), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.23), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 PHE 0.021 0.006 PHE A 94 TYR 0.009 0.003 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.12036 ( 44) hydrogen bonds : angle 6.24861 ( 132) covalent geometry : bond 0.00932 ( 2784) covalent geometry : angle 0.65055 ( 3762) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.280 Fit side-chains REVERT: A 43 LYS cc_start: 0.8300 (tttm) cc_final: 0.7746 (ttpt) REVERT: B 43 LYS cc_start: 0.8282 (tttm) cc_final: 0.7716 (ttpt) REVERT: C 43 LYS cc_start: 0.8572 (tttm) cc_final: 0.7972 (ttmt) REVERT: E 43 LYS cc_start: 0.8559 (tttm) cc_final: 0.7995 (ttpt) REVERT: E 58 LYS cc_start: 0.8999 (mttt) cc_final: 0.8731 (mttp) REVERT: D 43 LYS cc_start: 0.8330 (tttm) cc_final: 0.7748 (ttpt) REVERT: F 43 LYS cc_start: 0.8363 (tttm) cc_final: 0.7735 (ttmt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 1.0340 time to fit residues: 59.5341 Evaluate side-chains 53 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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: 0.6980 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 0.0670 chunk 28 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 65 ASN C 65 ASN E 65 ASN D 65 ASN D 87 ASN F 65 ASN F 87 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.103380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.088055 restraints weight = 3241.590| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.29 r_work: 0.3105 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2784 Z= 0.085 Angle : 0.362 2.724 3762 Z= 0.212 Chirality : 0.050 0.118 492 Planarity : 0.002 0.011 468 Dihedral : 3.532 10.161 396 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.74 % Allowed : 9.38 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.35), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.010 0.002 PHE A 94 TYR 0.016 0.001 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.00974 ( 44) hydrogen bonds : angle 4.22732 ( 132) covalent geometry : bond 0.00183 ( 2784) covalent geometry : angle 0.36151 ( 3762) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.326 Fit side-chains REVERT: A 43 LYS cc_start: 0.8441 (tttm) cc_final: 0.7803 (ttpt) REVERT: B 43 LYS cc_start: 0.8437 (tttm) cc_final: 0.7752 (ttpt) REVERT: C 43 LYS cc_start: 0.8776 (tttm) cc_final: 0.8116 (ttmt) REVERT: C 58 LYS cc_start: 0.9062 (mttt) cc_final: 0.8807 (mttp) REVERT: E 43 LYS cc_start: 0.8752 (tttm) cc_final: 0.8116 (ttpt) REVERT: E 58 LYS cc_start: 0.8986 (mttt) cc_final: 0.8739 (mttp) REVERT: D 43 LYS cc_start: 0.8445 (tttm) cc_final: 0.7767 (ttmt) REVERT: F 43 LYS cc_start: 0.8427 (tttm) cc_final: 0.7721 (ttmt) outliers start: 5 outliers final: 0 residues processed: 47 average time/residue: 1.1862 time to fit residues: 57.2532 Evaluate side-chains 40 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 87 ASN B 87 ASN C 65 ASN D 65 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.099770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.084376 restraints weight = 3325.028| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.30 r_work: 0.3051 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2784 Z= 0.143 Angle : 0.378 3.151 3762 Z= 0.217 Chirality : 0.049 0.115 492 Planarity : 0.002 0.009 468 Dihedral : 3.702 9.585 396 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.78 % Allowed : 12.15 % Favored : 85.07 % 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: -2.30 (0.38), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.013 0.004 PHE B 94 TYR 0.012 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.01058 ( 44) hydrogen bonds : angle 4.11848 ( 132) covalent geometry : bond 0.00334 ( 2784) covalent geometry : angle 0.37846 ( 3762) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.438 Fit side-chains REVERT: A 43 LYS cc_start: 0.8451 (tttm) cc_final: 0.7804 (ttpt) REVERT: B 43 LYS cc_start: 0.8473 (tttm) cc_final: 0.7802 (ttpt) REVERT: C 43 LYS cc_start: 0.8780 (tttm) cc_final: 0.8127 (ttmt) REVERT: E 43 LYS cc_start: 0.8759 (tttm) cc_final: 0.8137 (ttpt) REVERT: E 58 LYS cc_start: 0.9001 (mttt) cc_final: 0.8751 (mttp) REVERT: D 43 LYS cc_start: 0.8399 (tttm) cc_final: 0.7716 (ttmt) REVERT: F 43 LYS cc_start: 0.8375 (tttm) cc_final: 0.7680 (ttmt) outliers start: 8 outliers final: 1 residues processed: 43 average time/residue: 1.1963 time to fit residues: 53.0511 Evaluate side-chains 40 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.097493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.082118 restraints weight = 3428.114| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.31 r_work: 0.3000 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2784 Z= 0.252 Angle : 0.446 3.995 3762 Z= 0.254 Chirality : 0.049 0.115 492 Planarity : 0.002 0.011 468 Dihedral : 4.175 10.232 396 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.78 % Allowed : 13.19 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.38), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.018 0.005 PHE B 94 TYR 0.009 0.002 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.01286 ( 44) hydrogen bonds : angle 4.22101 ( 132) covalent geometry : bond 0.00591 ( 2784) covalent geometry : angle 0.44601 ( 3762) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.286 Fit side-chains REVERT: A 43 LYS cc_start: 0.8481 (tttm) cc_final: 0.7826 (ttpt) REVERT: B 43 LYS cc_start: 0.8480 (tttm) cc_final: 0.7808 (ttpt) REVERT: C 43 LYS cc_start: 0.8799 (tttm) cc_final: 0.8134 (ttmt) REVERT: E 43 LYS cc_start: 0.8792 (tttm) cc_final: 0.8166 (ttpt) REVERT: E 58 LYS cc_start: 0.9029 (mttt) cc_final: 0.8759 (mttp) REVERT: D 43 LYS cc_start: 0.8411 (tttm) cc_final: 0.7722 (ttmt) REVERT: F 43 LYS cc_start: 0.8359 (tttm) cc_final: 0.7664 (ttmt) outliers start: 8 outliers final: 1 residues processed: 48 average time/residue: 1.2374 time to fit residues: 60.9190 Evaluate side-chains 43 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 0.0570 chunk 29 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.100117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.084887 restraints weight = 3314.666| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.30 r_work: 0.3056 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2784 Z= 0.139 Angle : 0.370 2.847 3762 Z= 0.213 Chirality : 0.049 0.116 492 Planarity : 0.001 0.010 468 Dihedral : 3.850 10.490 396 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.69 % Allowed : 16.32 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.39), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.012 0.003 PHE B 94 TYR 0.005 0.001 TYR A 39 Details of bonding type rmsd hydrogen bonds : bond 0.00960 ( 44) hydrogen bonds : angle 4.06952 ( 132) covalent geometry : bond 0.00319 ( 2784) covalent geometry : angle 0.36956 ( 3762) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.281 Fit side-chains REVERT: A 43 LYS cc_start: 0.8474 (tttm) cc_final: 0.7793 (ttpt) REVERT: B 43 LYS cc_start: 0.8464 (tttm) cc_final: 0.7781 (ttpt) REVERT: C 34 LYS cc_start: 0.8640 (pttt) cc_final: 0.8436 (pttt) REVERT: C 43 LYS cc_start: 0.8780 (tttm) cc_final: 0.8123 (ttmt) REVERT: E 43 LYS cc_start: 0.8801 (tttm) cc_final: 0.8149 (ttmt) REVERT: E 58 LYS cc_start: 0.8980 (mttt) cc_final: 0.8721 (mttp) REVERT: D 43 LYS cc_start: 0.8380 (tttm) cc_final: 0.7689 (ttmt) REVERT: F 43 LYS cc_start: 0.8352 (tttm) cc_final: 0.7652 (ttmt) outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 1.1478 time to fit residues: 55.4344 Evaluate side-chains 44 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 65 ASN C 65 ASN F 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.097224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.081636 restraints weight = 3450.100| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.33 r_work: 0.2998 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.030 2784 Z= 0.282 Angle : 0.443 3.230 3762 Z= 0.255 Chirality : 0.050 0.115 492 Planarity : 0.002 0.012 468 Dihedral : 4.324 10.603 396 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.69 % Allowed : 17.71 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.39), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.019 0.005 PHE B 94 TYR 0.016 0.003 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.01298 ( 44) hydrogen bonds : angle 4.21051 ( 132) covalent geometry : bond 0.00658 ( 2784) covalent geometry : angle 0.44261 ( 3762) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.326 Fit side-chains REVERT: A 43 LYS cc_start: 0.8523 (tttm) cc_final: 0.7863 (ttpt) REVERT: B 43 LYS cc_start: 0.8498 (tttm) cc_final: 0.7832 (ttpt) REVERT: C 34 LYS cc_start: 0.8699 (pttt) cc_final: 0.8206 (pttt) REVERT: C 43 LYS cc_start: 0.8820 (tttm) cc_final: 0.8176 (ttmt) REVERT: C 83 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8242 (mt-10) REVERT: E 43 LYS cc_start: 0.8804 (tttm) cc_final: 0.8187 (ttpt) REVERT: E 58 LYS cc_start: 0.9042 (mttt) cc_final: 0.8772 (mttp) REVERT: D 43 LYS cc_start: 0.8405 (tttm) cc_final: 0.7708 (ttmt) REVERT: F 43 LYS cc_start: 0.8362 (tttm) cc_final: 0.7677 (ttmt) REVERT: F 79 GLN cc_start: 0.9206 (tt0) cc_final: 0.8938 (tt0) outliers start: 2 outliers final: 1 residues processed: 49 average time/residue: 1.1758 time to fit residues: 59.1681 Evaluate side-chains 43 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 26 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.098033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.082556 restraints weight = 3461.221| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.34 r_work: 0.3022 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 2784 Z= 0.210 Angle : 0.408 3.068 3762 Z= 0.236 Chirality : 0.049 0.116 492 Planarity : 0.002 0.013 468 Dihedral : 4.189 10.486 396 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.74 % Allowed : 17.36 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.39), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.016 0.004 PHE B 94 TYR 0.016 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.01135 ( 44) hydrogen bonds : angle 4.16322 ( 132) covalent geometry : bond 0.00484 ( 2784) covalent geometry : angle 0.40757 ( 3762) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.318 Fit side-chains REVERT: A 43 LYS cc_start: 0.8535 (tttm) cc_final: 0.7846 (ttpt) REVERT: B 43 LYS cc_start: 0.8470 (tttm) cc_final: 0.7787 (ttpt) REVERT: C 34 LYS cc_start: 0.8638 (pttt) cc_final: 0.8387 (pttt) REVERT: C 43 LYS cc_start: 0.8799 (tttm) cc_final: 0.8160 (ttmt) REVERT: E 34 LYS cc_start: 0.8372 (mttm) cc_final: 0.8035 (mtpt) REVERT: E 43 LYS cc_start: 0.8805 (tttm) cc_final: 0.8166 (ttmt) REVERT: E 58 LYS cc_start: 0.8989 (mttt) cc_final: 0.8717 (mttp) REVERT: D 43 LYS cc_start: 0.8393 (tttm) cc_final: 0.7712 (ttpt) REVERT: F 43 LYS cc_start: 0.8360 (tttm) cc_final: 0.7666 (ttmt) outliers start: 5 outliers final: 2 residues processed: 51 average time/residue: 1.0817 time to fit residues: 56.7173 Evaluate side-chains 46 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain D residue 44 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN C 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.098843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.083187 restraints weight = 3431.054| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.37 r_work: 0.3038 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2784 Z= 0.169 Angle : 0.390 2.861 3762 Z= 0.226 Chirality : 0.049 0.115 492 Planarity : 0.002 0.012 468 Dihedral : 4.048 10.400 396 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.39 % Allowed : 17.01 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.40), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.014 0.004 PHE B 94 TYR 0.017 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.01021 ( 44) hydrogen bonds : angle 4.10978 ( 132) covalent geometry : bond 0.00388 ( 2784) covalent geometry : angle 0.39032 ( 3762) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.284 Fit side-chains REVERT: A 43 LYS cc_start: 0.8510 (tttm) cc_final: 0.7816 (ttpt) REVERT: B 43 LYS cc_start: 0.8440 (tttm) cc_final: 0.7753 (ttpt) REVERT: C 43 LYS cc_start: 0.8802 (tttm) cc_final: 0.8155 (ttmt) REVERT: E 43 LYS cc_start: 0.8795 (tttm) cc_final: 0.8105 (ttmt) REVERT: E 58 LYS cc_start: 0.8999 (mttt) cc_final: 0.8742 (mttp) REVERT: D 43 LYS cc_start: 0.8363 (tttm) cc_final: 0.7689 (ttpt) REVERT: F 43 LYS cc_start: 0.8343 (tttm) cc_final: 0.7644 (ttmt) outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 1.1297 time to fit residues: 54.5758 Evaluate side-chains 47 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain D residue 98 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 0.3980 chunk 6 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.103884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.088916 restraints weight = 3309.045| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.26 r_work: 0.3138 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2784 Z= 0.075 Angle : 0.332 3.185 3762 Z= 0.194 Chirality : 0.049 0.115 492 Planarity : 0.001 0.011 468 Dihedral : 3.479 9.304 396 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 0.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.04 % Allowed : 17.71 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.41), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.008 0.002 PHE B 94 TYR 0.014 0.001 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.00773 ( 44) hydrogen bonds : angle 3.87628 ( 132) covalent geometry : bond 0.00160 ( 2784) covalent geometry : angle 0.33190 ( 3762) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.309 Fit side-chains REVERT: A 43 LYS cc_start: 0.8506 (tttm) cc_final: 0.7829 (ttpt) REVERT: B 43 LYS cc_start: 0.8455 (tttm) cc_final: 0.7790 (ttpt) REVERT: C 43 LYS cc_start: 0.8809 (tttm) cc_final: 0.8170 (ttmt) REVERT: E 43 LYS cc_start: 0.8794 (tttm) cc_final: 0.8109 (ttmt) REVERT: E 58 LYS cc_start: 0.8957 (mttt) cc_final: 0.8697 (mttp) REVERT: D 43 LYS cc_start: 0.8392 (tttm) cc_final: 0.7745 (ttmt) REVERT: F 43 LYS cc_start: 0.8381 (tttm) cc_final: 0.7695 (ttmt) outliers start: 3 outliers final: 2 residues processed: 50 average time/residue: 1.0693 time to fit residues: 55.1013 Evaluate side-chains 46 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain E residue 42 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 23 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 27 optimal weight: 0.0370 chunk 8 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 overall best weight: 2.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 65 ASN E 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.099447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.083617 restraints weight = 3407.553| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.31 r_work: 0.3051 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 2784 Z= 0.195 Angle : 0.395 2.820 3762 Z= 0.229 Chirality : 0.049 0.116 492 Planarity : 0.002 0.012 468 Dihedral : 4.031 10.605 396 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.69 % Allowed : 20.14 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.41), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.015 0.004 PHE B 94 TYR 0.017 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.01044 ( 44) hydrogen bonds : angle 4.09118 ( 132) covalent geometry : bond 0.00452 ( 2784) covalent geometry : angle 0.39500 ( 3762) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.287 Fit side-chains REVERT: A 43 LYS cc_start: 0.8515 (tttm) cc_final: 0.7863 (ttpt) REVERT: B 43 LYS cc_start: 0.8444 (tttm) cc_final: 0.7779 (ttpt) REVERT: C 43 LYS cc_start: 0.8807 (tttm) cc_final: 0.8167 (ttmt) REVERT: E 43 LYS cc_start: 0.8819 (tttm) cc_final: 0.8156 (ttmt) REVERT: E 58 LYS cc_start: 0.9009 (mttt) cc_final: 0.8733 (mttp) REVERT: D 43 LYS cc_start: 0.8361 (tttm) cc_final: 0.7699 (ttpt) REVERT: F 43 LYS cc_start: 0.8335 (tttm) cc_final: 0.7645 (ttmt) outliers start: 2 outliers final: 2 residues processed: 45 average time/residue: 1.1616 time to fit residues: 53.6911 Evaluate side-chains 45 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain E residue 42 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 26 optimal weight: 0.0470 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.101094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.085512 restraints weight = 3257.177| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.25 r_work: 0.3097 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2784 Z= 0.125 Angle : 0.363 3.481 3762 Z= 0.210 Chirality : 0.049 0.115 492 Planarity : 0.001 0.013 468 Dihedral : 3.808 10.135 396 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.69 % Allowed : 20.14 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.41), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.011 0.003 PHE B 94 TYR 0.015 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.00920 ( 44) hydrogen bonds : angle 4.01178 ( 132) covalent geometry : bond 0.00284 ( 2784) covalent geometry : angle 0.36266 ( 3762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2291.14 seconds wall clock time: 39 minutes 55.43 seconds (2395.43 seconds total)