Starting phenix.real_space_refine on Wed Sep 17 03:17:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lon_63250/09_2025/9lon_63250.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lon_63250/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9lon_63250/09_2025/9lon_63250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lon_63250/09_2025/9lon_63250.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lon_63250/09_2025/9lon_63250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lon_63250/09_2025/9lon_63250.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: B, C, E, D, F Time building chain proxies: 0.53, per 1000 atoms: 0.19 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: 0.14 Conformation dependent library (CDL) restraints added in 116.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.08 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: 0.22 Time building geometry restraints manager: 0.22 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.410 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.020 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.50 (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 TYR 0.009 0.003 TYR D 39 PHE 0.021 0.006 PHE A 94 HIS 0.002 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00932 ( 2784) covalent geometry : angle 0.65055 ( 3762) hydrogen bonds : bond 0.12036 ( 44) hydrogen bonds : angle 6.24861 ( 132) *********************** 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 : 0.071 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: 0.4348 time to fit residues: 25.0068 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 : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.102442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.086794 restraints weight = 3346.817| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.34 r_work: 0.3086 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1426 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= 0.101 Angle : 0.368 2.708 3762 Z= 0.215 Chirality : 0.050 0.119 492 Planarity : 0.002 0.011 468 Dihedral : 3.579 10.013 396 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.78 (0.34), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.001 TYR E 39 PHE 0.011 0.003 PHE A 94 HIS 0.001 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 2784) covalent geometry : angle 0.36752 ( 3762) hydrogen bonds : bond 0.01102 ( 44) hydrogen bonds : angle 4.26018 ( 132) *********************** 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 50 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.107 Fit side-chains REVERT: A 43 LYS cc_start: 0.8455 (tttm) cc_final: 0.7819 (ttpt) REVERT: B 43 LYS cc_start: 0.8464 (tttm) cc_final: 0.7778 (ttpt) REVERT: C 43 LYS cc_start: 0.8801 (tttm) cc_final: 0.8147 (ttmt) REVERT: C 58 LYS cc_start: 0.9077 (mttt) cc_final: 0.8777 (mttp) REVERT: E 43 LYS cc_start: 0.8756 (tttm) cc_final: 0.8123 (ttpt) REVERT: E 58 LYS cc_start: 0.9008 (mttt) cc_final: 0.8751 (mttp) REVERT: D 43 LYS cc_start: 0.8451 (tttm) cc_final: 0.7804 (ttpt) REVERT: F 43 LYS cc_start: 0.8414 (tttm) cc_final: 0.7705 (ttmt) outliers start: 5 outliers final: 0 residues processed: 46 average time/residue: 0.5126 time to fit residues: 24.2253 Evaluate side-chains 39 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 27 optimal weight: 0.0870 chunk 30 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- 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 D 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.099838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.084011 restraints weight = 3408.494| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.39 r_work: 0.3047 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2784 Z= 0.147 Angle : 0.386 3.149 3762 Z= 0.220 Chirality : 0.049 0.115 492 Planarity : 0.002 0.009 468 Dihedral : 3.725 9.572 396 Min Nonbonded Distance : 2.566 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.37), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR E 39 PHE 0.013 0.004 PHE B 94 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 2784) covalent geometry : angle 0.38608 ( 3762) hydrogen bonds : bond 0.01047 ( 44) hydrogen bonds : angle 4.13446 ( 132) *********************** 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 51 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.102 Fit side-chains REVERT: A 43 LYS cc_start: 0.8423 (tttm) cc_final: 0.7777 (ttpt) REVERT: B 43 LYS cc_start: 0.8458 (tttm) cc_final: 0.7773 (ttpt) REVERT: C 34 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8175 (mttt) REVERT: C 43 LYS cc_start: 0.8779 (tttm) cc_final: 0.8120 (ttmt) REVERT: E 43 LYS cc_start: 0.8752 (tttm) cc_final: 0.8120 (ttpt) REVERT: E 58 LYS cc_start: 0.8993 (mttt) cc_final: 0.8740 (mttp) REVERT: D 43 LYS cc_start: 0.8379 (tttm) cc_final: 0.7691 (ttmt) REVERT: F 43 LYS cc_start: 0.8365 (tttm) cc_final: 0.7661 (ttmt) outliers start: 8 outliers final: 1 residues processed: 45 average time/residue: 0.5610 time to fit residues: 25.8491 Evaluate side-chains 42 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LYS 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 8 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3402 r_free = 0.3402 target = 0.097994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.082423 restraints weight = 3404.513| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.32 r_work: 0.3010 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 2784 Z= 0.242 Angle : 0.444 3.631 3762 Z= 0.251 Chirality : 0.049 0.115 492 Planarity : 0.002 0.011 468 Dihedral : 4.131 10.135 396 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.78 % Allowed : 13.54 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.38), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR F 39 PHE 0.017 0.005 PHE F 94 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00566 ( 2784) covalent geometry : angle 0.44420 ( 3762) hydrogen bonds : bond 0.01249 ( 44) hydrogen bonds : angle 4.21170 ( 132) *********************** 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 53 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.121 Fit side-chains REVERT: A 43 LYS cc_start: 0.8460 (tttm) cc_final: 0.7813 (ttpt) REVERT: B 43 LYS cc_start: 0.8494 (tttm) cc_final: 0.7823 (ttpt) REVERT: C 43 LYS cc_start: 0.8811 (tttm) cc_final: 0.8151 (ttmt) REVERT: E 43 LYS cc_start: 0.8792 (tttm) cc_final: 0.8166 (ttpt) REVERT: E 58 LYS cc_start: 0.9027 (mttt) cc_final: 0.8756 (mttp) REVERT: D 43 LYS cc_start: 0.8416 (tttm) cc_final: 0.7736 (ttmt) REVERT: F 43 LYS cc_start: 0.8374 (tttm) cc_final: 0.7682 (ttmt) outliers start: 8 outliers final: 1 residues processed: 48 average time/residue: 0.6279 time to fit residues: 30.8549 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 : 0.130 ------------------------------------------------------------------------------- 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 14 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.100191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.084493 restraints weight = 3345.287| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.37 r_work: 0.3054 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1581 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= 0.145 Angle : 0.370 2.537 3762 Z= 0.213 Chirality : 0.049 0.116 492 Planarity : 0.002 0.010 468 Dihedral : 3.850 10.065 396 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.04 % Allowed : 16.32 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 TYR 0.016 0.002 TYR E 39 PHE 0.012 0.004 PHE B 94 HIS 0.001 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 2784) covalent geometry : angle 0.36959 ( 3762) hydrogen bonds : bond 0.00962 ( 44) hydrogen bonds : angle 4.06014 ( 132) *********************** 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 47 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.117 Fit side-chains REVERT: A 43 LYS cc_start: 0.8463 (tttm) cc_final: 0.7778 (ttpt) REVERT: B 43 LYS cc_start: 0.8450 (tttm) cc_final: 0.7763 (ttpt) REVERT: C 43 LYS cc_start: 0.8806 (tttm) cc_final: 0.8143 (ttmt) REVERT: E 43 LYS cc_start: 0.8795 (tttm) cc_final: 0.8138 (ttmt) REVERT: E 58 LYS cc_start: 0.8973 (mttt) cc_final: 0.8712 (mttp) REVERT: D 43 LYS cc_start: 0.8368 (tttm) cc_final: 0.7675 (ttmt) REVERT: F 43 LYS cc_start: 0.8370 (tttm) cc_final: 0.7660 (ttmt) outliers start: 3 outliers final: 1 residues processed: 45 average time/residue: 0.6027 time to fit residues: 27.7425 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 : 0.106 ------------------------------------------------------------------------------- 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 17 optimal weight: 7.9990 chunk 5 optimal weight: 0.0050 chunk 26 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 overall best weight: 4.0002 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.096991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.081253 restraints weight = 3448.732| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.35 r_work: 0.2993 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 2784 Z= 0.297 Angle : 0.454 3.434 3762 Z= 0.261 Chirality : 0.050 0.115 492 Planarity : 0.002 0.012 468 Dihedral : 4.366 10.650 396 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.35 % Allowed : 17.36 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.39), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR F 39 PHE 0.019 0.005 PHE B 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00694 ( 2784) covalent geometry : angle 0.45377 ( 3762) hydrogen bonds : bond 0.01325 ( 44) hydrogen bonds : angle 4.23728 ( 132) *********************** 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 48 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.111 Fit side-chains REVERT: A 43 LYS cc_start: 0.8521 (tttm) cc_final: 0.7858 (ttpt) REVERT: B 43 LYS cc_start: 0.8497 (tttm) cc_final: 0.7831 (ttpt) REVERT: C 34 LYS cc_start: 0.8631 (mttt) cc_final: 0.8391 (mtpt) REVERT: C 43 LYS cc_start: 0.8825 (tttm) cc_final: 0.8177 (ttmt) REVERT: E 43 LYS cc_start: 0.8805 (tttm) cc_final: 0.8173 (ttpt) REVERT: E 58 LYS cc_start: 0.9048 (mttt) cc_final: 0.8787 (mttp) REVERT: D 43 LYS cc_start: 0.8401 (tttm) cc_final: 0.7702 (ttmt) REVERT: F 43 LYS cc_start: 0.8357 (tttm) cc_final: 0.7668 (ttmt) outliers start: 1 outliers final: 1 residues processed: 48 average time/residue: 0.6046 time to fit residues: 29.7388 Evaluate side-chains 45 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.069 ------------------------------------------------------------------------------- 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 12 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.099026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.083389 restraints weight = 3394.438| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.34 r_work: 0.3043 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2784 Z= 0.163 Angle : 0.387 2.998 3762 Z= 0.224 Chirality : 0.049 0.116 492 Planarity : 0.002 0.012 468 Dihedral : 4.011 10.292 396 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.40), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR E 39 PHE 0.013 0.004 PHE B 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 2784) covalent geometry : angle 0.38739 ( 3762) hydrogen bonds : bond 0.01022 ( 44) hydrogen bonds : angle 4.10039 ( 132) *********************** 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 : 0.106 Fit side-chains REVERT: A 43 LYS cc_start: 0.8502 (tttm) cc_final: 0.7816 (ttpt) REVERT: B 43 LYS cc_start: 0.8457 (tttm) cc_final: 0.7780 (ttpt) REVERT: C 34 LYS cc_start: 0.8536 (mttt) cc_final: 0.8307 (mtpt) REVERT: C 43 LYS cc_start: 0.8818 (tttm) cc_final: 0.8169 (ttmt) REVERT: E 43 LYS cc_start: 0.8800 (tttm) cc_final: 0.8165 (ttmt) REVERT: E 58 LYS cc_start: 0.8990 (mttt) cc_final: 0.8730 (mttp) REVERT: D 43 LYS cc_start: 0.8393 (tttm) cc_final: 0.7725 (ttpt) REVERT: F 43 LYS cc_start: 0.8362 (tttm) cc_final: 0.7665 (ttmt) outliers start: 5 outliers final: 2 residues processed: 51 average time/residue: 0.4770 time to fit residues: 24.9799 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 : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain E residue 42 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.101090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.085472 restraints weight = 3371.224| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.32 r_work: 0.3085 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1746 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= 0.111 Angle : 0.352 3.316 3762 Z= 0.205 Chirality : 0.049 0.116 492 Planarity : 0.001 0.011 468 Dihedral : 3.729 9.927 396 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.41), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR B 39 PHE 0.011 0.003 PHE B 94 HIS 0.001 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 2784) covalent geometry : angle 0.35167 ( 3762) hydrogen bonds : bond 0.00860 ( 44) hydrogen bonds : angle 3.96404 ( 132) *********************** 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 51 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.110 Fit side-chains REVERT: A 43 LYS cc_start: 0.8489 (tttm) cc_final: 0.7807 (ttpt) REVERT: B 43 LYS cc_start: 0.8459 (tttm) cc_final: 0.7778 (ttpt) REVERT: C 43 LYS cc_start: 0.8804 (tttm) cc_final: 0.8157 (ttmt) REVERT: E 43 LYS cc_start: 0.8801 (tttm) cc_final: 0.8111 (ttmt) REVERT: E 58 LYS cc_start: 0.8973 (mttt) cc_final: 0.8707 (mttp) REVERT: D 43 LYS cc_start: 0.8396 (tttm) cc_final: 0.7737 (ttpt) REVERT: F 43 LYS cc_start: 0.8384 (tttm) cc_final: 0.7682 (ttmt) outliers start: 4 outliers final: 3 residues processed: 50 average time/residue: 0.4847 time to fit residues: 24.8644 Evaluate side-chains 48 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.085 ------------------------------------------------------------------------------- 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 5 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 0.0170 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.098829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.083034 restraints weight = 3503.448| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.38 r_work: 0.3040 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2784 Z= 0.170 Angle : 0.385 3.319 3762 Z= 0.223 Chirality : 0.049 0.116 492 Planarity : 0.002 0.013 468 Dihedral : 3.978 10.596 396 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.04 % Allowed : 18.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.41), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR B 39 PHE 0.014 0.004 PHE B 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 2784) covalent geometry : angle 0.38511 ( 3762) hydrogen bonds : bond 0.01015 ( 44) hydrogen bonds : angle 4.04482 ( 132) *********************** 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 49 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.071 Fit side-chains REVERT: A 43 LYS cc_start: 0.8478 (tttm) cc_final: 0.7806 (ttpt) REVERT: B 43 LYS cc_start: 0.8434 (tttm) cc_final: 0.7760 (ttpt) REVERT: C 43 LYS cc_start: 0.8796 (tttm) cc_final: 0.8147 (ttmt) REVERT: E 43 LYS cc_start: 0.8813 (tttm) cc_final: 0.8128 (ttmt) REVERT: E 58 LYS cc_start: 0.8975 (mttt) cc_final: 0.8718 (mttp) REVERT: D 43 LYS cc_start: 0.8377 (tttm) cc_final: 0.7703 (ttpt) REVERT: F 43 LYS cc_start: 0.8363 (tttm) cc_final: 0.7666 (ttmt) outliers start: 3 outliers final: 2 residues processed: 48 average time/residue: 0.5530 time to fit residues: 27.2210 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 : 0.109 ------------------------------------------------------------------------------- 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 17 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.099553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.083830 restraints weight = 3444.957| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.35 r_work: 0.3053 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1696 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= 0.151 Angle : 0.380 3.220 3762 Z= 0.219 Chirality : 0.049 0.115 492 Planarity : 0.002 0.013 468 Dihedral : 3.929 10.264 396 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.04 % Allowed : 18.40 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.41), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR B 39 PHE 0.013 0.003 PHE B 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 2784) covalent geometry : angle 0.37997 ( 3762) hydrogen bonds : bond 0.00971 ( 44) hydrogen bonds : angle 4.03521 ( 132) ********************** 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 48 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.087 Fit side-chains REVERT: A 43 LYS cc_start: 0.8495 (tttm) cc_final: 0.7822 (ttpt) REVERT: B 43 LYS cc_start: 0.8443 (tttm) cc_final: 0.7774 (ttpt) REVERT: C 43 LYS cc_start: 0.8771 (tttm) cc_final: 0.8132 (ttmt) REVERT: E 43 LYS cc_start: 0.8810 (tttm) cc_final: 0.8131 (ttmt) REVERT: E 58 LYS cc_start: 0.8987 (mttt) cc_final: 0.8733 (mttp) REVERT: D 43 LYS cc_start: 0.8372 (tttm) cc_final: 0.7711 (ttpt) REVERT: F 43 LYS cc_start: 0.8357 (tttm) cc_final: 0.7660 (ttmt) outliers start: 3 outliers final: 2 residues processed: 48 average time/residue: 0.5111 time to fit residues: 25.1729 Evaluate side-chains 47 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.113 ------------------------------------------------------------------------------- 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 8 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 0.0870 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 E 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.104871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.089864 restraints weight = 3281.735| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.28 r_work: 0.3168 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 2784 Z= 0.065 Angle : 0.325 3.191 3762 Z= 0.190 Chirality : 0.049 0.117 492 Planarity : 0.001 0.011 468 Dihedral : 3.380 9.114 396 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 0.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.69 % Allowed : 19.44 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.42), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR B 39 PHE 0.007 0.002 PHE A 94 HIS 0.001 0.000 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00135 ( 2784) covalent geometry : angle 0.32486 ( 3762) hydrogen bonds : bond 0.00745 ( 44) hydrogen bonds : angle 3.82265 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1110.20 seconds wall clock time: 19 minutes 40.18 seconds (1180.18 seconds total)