Starting phenix.real_space_refine on Tue Feb 3 15:14:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a7p_15223/02_2026/8a7p_15223.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a7p_15223/02_2026/8a7p_15223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a7p_15223/02_2026/8a7p_15223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a7p_15223/02_2026/8a7p_15223.map" model { file = "/net/cci-nas-00/data/ceres_data/8a7p_15223/02_2026/8a7p_15223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a7p_15223/02_2026/8a7p_15223.cif" } resolution = 3.4 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= 0.001 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: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2760 2.51 5 N 708 2.21 5 O 834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4320 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 720 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 4, 'TRANS': 82} Chain: "B" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 720 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 4, 'TRANS': 82} Chain: "C" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 720 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 4, 'TRANS': 82} Chain: "D" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 720 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 4, 'TRANS': 82} Chain: "E" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 720 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 4, 'TRANS': 82} Chain: "F" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 720 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 4, 'TRANS': 82} Time building chain proxies: 1.19, per 1000 atoms: 0.28 Number of scatterers: 4320 At special positions: 0 Unit cell: (155.21, 104.58, 33.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 834 8.00 N 708 7.00 C 2760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 80 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 80 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 80 " distance=2.03 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS E 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 80 " distance=2.03 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: 0.32 Conformation dependent library (CDL) restraints added in 158.4 milliseconds 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1008 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 46.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 12 removed outlier: 6.605A pdb=" N GLN A 8 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N SER C 11 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR A 10 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN C 8 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N SER E 11 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N TYR C 10 " --> pdb=" O SER E 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 22 removed outlier: 6.956A pdb=" N ASN C 21 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN E 21 " --> pdb=" O SER C 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 39 removed outlier: 6.908A pdb=" N ASP C 34 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP E 34 " --> pdb=" O SER C 33 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 42 through 49 removed outlier: 6.771A pdb=" N ILE C 46 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU A 47 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE E 46 " --> pdb=" O ARG C 45 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU C 47 " --> pdb=" O ILE E 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 52 through 53 removed outlier: 6.818A pdb=" N SER A 52 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N SER C 52 " --> pdb=" O ASP E 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 59 through 66 removed outlier: 7.094A pdb=" N TYR C 63 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU A 64 " --> pdb=" O TYR C 63 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU C 65 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR A 66 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR E 63 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU C 64 " --> pdb=" O TYR E 63 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU E 65 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N TYR C 66 " --> pdb=" O LEU E 65 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AA9, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AB1, first strand: chain 'A' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'A' and resid 81 through 83 Processing sheet with id=AB3, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AB4, first strand: chain 'B' and resid 7 through 12 removed outlier: 6.450A pdb=" N GLN B 8 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N SER D 11 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N TYR B 10 " --> pdb=" O SER D 11 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 15 through 17 Processing sheet with id=AB6, first strand: chain 'B' and resid 20 through 22 removed outlier: 6.832A pdb=" N ASN D 21 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN F 21 " --> pdb=" O SER D 20 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 33 through 39 removed outlier: 6.842A pdb=" N ASP D 34 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASP F 34 " --> pdb=" O SER D 33 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 42 through 53 removed outlier: 6.831A pdb=" N ILE D 46 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU B 47 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N SER D 52 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASP B 53 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE F 46 " --> pdb=" O ARG D 45 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU D 47 " --> pdb=" O ILE F 46 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 53 removed outlier: 6.831A pdb=" N ILE D 46 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU B 47 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N SER D 52 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASP B 53 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N ASP F 53 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER D 52 " --> pdb=" O ASP F 53 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 59 through 66 removed outlier: 7.010A pdb=" N TYR D 63 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU B 64 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU D 65 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N TYR B 66 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR F 63 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU D 64 " --> pdb=" O TYR F 63 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU F 65 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TYR D 66 " --> pdb=" O LEU F 65 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 69 through 70 Processing sheet with id=AC3, first strand: chain 'B' and resid 73 through 74 Processing sheet with id=AC4, first strand: chain 'B' and resid 77 through 78 Processing sheet with id=AC5, first strand: chain 'B' and resid 81 through 83 Processing sheet with id=AC6, first strand: chain 'B' and resid 86 through 88 removed outlier: 6.304A pdb=" N LEU D 87 " --> pdb=" O SER F 88 " (cutoff:3.500A) 100 hydrogen bonds defined for protein. 300 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: 0.58 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1380 1.34 - 1.46: 988 1.46 - 1.58: 2048 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 4440 Sorted by residual: bond pdb=" CA ALA F 79 " pdb=" C ALA F 79 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.61e-02 3.86e+03 4.73e-01 bond pdb=" CA ALA B 79 " pdb=" C ALA B 79 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.61e-02 3.86e+03 4.09e-01 bond pdb=" CA ALA A 79 " pdb=" C ALA A 79 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.61e-02 3.86e+03 3.91e-01 bond pdb=" CA ALA E 79 " pdb=" C ALA E 79 " ideal model delta sigma weight residual 1.523 1.532 -0.010 1.61e-02 3.86e+03 3.66e-01 bond pdb=" CA ALA C 79 " pdb=" C ALA C 79 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.61e-02 3.86e+03 3.44e-01 ... (remaining 4435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.75: 5327 0.75 - 1.51: 548 1.51 - 2.26: 78 2.26 - 3.01: 29 3.01 - 3.76: 30 Bond angle restraints: 6012 Sorted by residual: angle pdb=" C PRO C 14 " pdb=" N ALA C 15 " pdb=" CA ALA C 15 " ideal model delta sigma weight residual 121.94 118.18 3.76 1.76e+00 3.23e-01 4.58e+00 angle pdb=" C PRO E 14 " pdb=" N ALA E 15 " pdb=" CA ALA E 15 " ideal model delta sigma weight residual 121.94 118.19 3.75 1.76e+00 3.23e-01 4.55e+00 angle pdb=" C PRO B 14 " pdb=" N ALA B 15 " pdb=" CA ALA B 15 " ideal model delta sigma weight residual 121.94 118.23 3.71 1.76e+00 3.23e-01 4.44e+00 angle pdb=" C PRO A 14 " pdb=" N ALA A 15 " pdb=" CA ALA A 15 " ideal model delta sigma weight residual 121.94 118.24 3.70 1.76e+00 3.23e-01 4.41e+00 angle pdb=" C PRO D 14 " pdb=" N ALA D 15 " pdb=" CA ALA D 15 " ideal model delta sigma weight residual 121.94 118.26 3.68 1.76e+00 3.23e-01 4.38e+00 ... (remaining 6007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.54: 2461 13.54 - 27.07: 135 27.07 - 40.61: 32 40.61 - 54.15: 15 54.15 - 67.69: 9 Dihedral angle restraints: 2652 sinusoidal: 1092 harmonic: 1560 Sorted by residual: dihedral pdb=" N LYS E 58 " pdb=" CA LYS E 58 " pdb=" CB LYS E 58 " pdb=" CG LYS E 58 " ideal model delta sinusoidal sigma weight residual -60.00 -103.10 43.10 3 1.50e+01 4.44e-03 7.74e+00 dihedral pdb=" N LYS C 58 " pdb=" CA LYS C 58 " pdb=" CB LYS C 58 " pdb=" CG LYS C 58 " ideal model delta sinusoidal sigma weight residual -60.00 -103.08 43.08 3 1.50e+01 4.44e-03 7.74e+00 dihedral pdb=" N LYS A 58 " pdb=" CA LYS A 58 " pdb=" CB LYS A 58 " pdb=" CG LYS A 58 " ideal model delta sinusoidal sigma weight residual -60.00 -103.04 43.04 3 1.50e+01 4.44e-03 7.73e+00 ... (remaining 2649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 366 0.028 - 0.056: 174 0.056 - 0.085: 30 0.085 - 0.113: 35 0.113 - 0.141: 25 Chirality restraints: 630 Sorted by residual: chirality pdb=" CA PRO D 14 " pdb=" N PRO D 14 " pdb=" C PRO D 14 " pdb=" CB PRO D 14 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA PRO E 14 " pdb=" N PRO E 14 " pdb=" C PRO E 14 " pdb=" CB PRO E 14 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA PRO A 14 " pdb=" N PRO A 14 " pdb=" C PRO A 14 " pdb=" CB PRO A 14 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 627 not shown) Planarity restraints: 774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 13 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO B 14 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 14 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 14 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 13 " 0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO D 14 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 13 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.82e+00 pdb=" N PRO F 14 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO F 14 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 14 " 0.027 5.00e-02 4.00e+02 ... (remaining 771 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1137 2.83 - 3.35: 3283 3.35 - 3.87: 7097 3.87 - 4.38: 7181 4.38 - 4.90: 14250 Nonbonded interactions: 32948 Sorted by model distance: nonbonded pdb=" O LYS C 58 " pdb=" N LYS E 58 " model vdw 2.313 3.120 nonbonded pdb=" O LYS B 58 " pdb=" N LYS D 58 " model vdw 2.338 3.120 nonbonded pdb=" O LYS A 58 " pdb=" N LYS C 58 " model vdw 2.346 3.120 nonbonded pdb=" O LYS D 58 " pdb=" N LYS F 58 " model vdw 2.375 3.120 nonbonded pdb=" OE1 GLU C 47 " pdb=" NH1 ARG D 45 " model vdw 2.546 3.120 ... (remaining 32943 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 4.240 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: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.060 Find NCS groups from input model: 0.180 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: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 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 : 0.002 0.014 4446 Z= 0.111 Angle : 0.545 3.765 6024 Z= 0.326 Chirality : 0.044 0.141 630 Planarity : 0.005 0.049 774 Dihedral : 10.478 67.686 1626 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.83 % Allowed : 1.22 % Favored : 96.95 % 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 are not related in a simple way. whole: -3.55 (0.30), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.23), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 12 TYR 0.006 0.001 TYR D 63 PHE 0.012 0.002 PHE A 22 TRP 0.001 0.000 TRP B 60 HIS 0.003 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 4440) covalent geometry : angle 0.54480 ( 6012) SS BOND : bond 0.00171 ( 6) SS BOND : angle 0.55682 ( 12) hydrogen bonds : bond 0.23586 ( 93) hydrogen bonds : angle 9.70446 ( 300) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.202 Fit side-chains REVERT: B 89 GLN cc_start: 0.6643 (tt0) cc_final: 0.6005 (mt0) REVERT: D 89 GLN cc_start: 0.6838 (tt0) cc_final: 0.6041 (mt0) REVERT: E 53 ASP cc_start: 0.7895 (t0) cc_final: 0.7664 (t0) REVERT: F 89 GLN cc_start: 0.6597 (tt0) cc_final: 0.6134 (mt0) outliers start: 9 outliers final: 3 residues processed: 126 average time/residue: 0.0729 time to fit residues: 11.3289 Evaluate side-chains 67 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain F residue 49 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS A 84 HIS B 31 HIS C 31 HIS C 84 HIS D 31 HIS D 84 HIS E 31 HIS E 84 HIS E 89 GLN F 31 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.132267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.110882 restraints weight = 7190.289| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 3.06 r_work: 0.3984 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 4446 Z= 0.281 Angle : 0.780 5.900 6024 Z= 0.444 Chirality : 0.053 0.159 630 Planarity : 0.006 0.052 774 Dihedral : 6.146 30.123 573 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.44 % Allowed : 10.77 % Favored : 86.79 % 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 are not related in a simple way. whole: -3.43 (0.26), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.20), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 45 TYR 0.021 0.004 TYR F 26 PHE 0.024 0.003 PHE D 22 TRP 0.012 0.003 TRP C 60 HIS 0.007 0.002 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00637 ( 4440) covalent geometry : angle 0.78053 ( 6012) SS BOND : bond 0.00342 ( 6) SS BOND : angle 0.62351 ( 12) hydrogen bonds : bond 0.04994 ( 93) hydrogen bonds : angle 6.48138 ( 300) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.107 Fit side-chains REVERT: A 38 ASP cc_start: 0.8776 (p0) cc_final: 0.8555 (p0) REVERT: B 20 SER cc_start: 0.9035 (p) cc_final: 0.8819 (p) REVERT: B 45 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7496 (mtm180) REVERT: B 89 GLN cc_start: 0.6797 (tt0) cc_final: 0.5871 (mt0) REVERT: C 38 ASP cc_start: 0.8589 (p0) cc_final: 0.8348 (p0) REVERT: E 16 GLU cc_start: 0.6763 (mp0) cc_final: 0.6107 (tp30) REVERT: E 50 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7653 (mp0) REVERT: E 53 ASP cc_start: 0.8101 (t0) cc_final: 0.7853 (t0) REVERT: F 76 ASP cc_start: 0.8311 (m-30) cc_final: 0.8103 (m-30) REVERT: F 89 GLN cc_start: 0.6259 (tt0) cc_final: 0.5878 (mt0) outliers start: 12 outliers final: 9 residues processed: 88 average time/residue: 0.0367 time to fit residues: 4.4203 Evaluate side-chains 75 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 55 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS E 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.127513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.105269 restraints weight = 7327.338| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 3.37 r_work: 0.4026 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4446 Z= 0.142 Angle : 0.626 5.679 6024 Z= 0.350 Chirality : 0.048 0.144 630 Planarity : 0.004 0.048 774 Dihedral : 5.759 24.967 573 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.24 % Allowed : 14.43 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 45 TYR 0.014 0.002 TYR E 67 PHE 0.020 0.002 PHE D 22 TRP 0.002 0.000 TRP F 60 HIS 0.002 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4440) covalent geometry : angle 0.62686 ( 6012) SS BOND : bond 0.00270 ( 6) SS BOND : angle 0.20945 ( 12) hydrogen bonds : bond 0.03690 ( 93) hydrogen bonds : angle 5.87388 ( 300) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.109 Fit side-chains REVERT: A 34 ASP cc_start: 0.8398 (m-30) cc_final: 0.8006 (m-30) REVERT: A 36 GLU cc_start: 0.8541 (tt0) cc_final: 0.8259 (tt0) REVERT: A 38 ASP cc_start: 0.8647 (p0) cc_final: 0.8125 (p0) REVERT: A 40 LEU cc_start: 0.9147 (tp) cc_final: 0.8760 (tt) REVERT: B 45 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7778 (mtm-85) REVERT: B 89 GLN cc_start: 0.6725 (tt0) cc_final: 0.5865 (mt0) REVERT: C 38 ASP cc_start: 0.8403 (p0) cc_final: 0.7906 (p0) REVERT: D 45 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7468 (ttm170) REVERT: E 16 GLU cc_start: 0.6437 (mp0) cc_final: 0.6029 (tp30) REVERT: E 22 PHE cc_start: 0.7957 (p90) cc_final: 0.7713 (p90) REVERT: E 50 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7486 (mp0) REVERT: F 89 GLN cc_start: 0.6148 (tt0) cc_final: 0.5747 (mt0) outliers start: 11 outliers final: 8 residues processed: 80 average time/residue: 0.0445 time to fit residues: 4.6196 Evaluate side-chains 78 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 55 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 23 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 21 optimal weight: 7.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.126953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.104724 restraints weight = 7327.507| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 3.40 r_work: 0.4007 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4446 Z= 0.138 Angle : 0.617 7.057 6024 Z= 0.344 Chirality : 0.048 0.143 630 Planarity : 0.004 0.043 774 Dihedral : 5.683 25.548 573 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.44 % Allowed : 16.06 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.28), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 45 TYR 0.012 0.002 TYR E 67 PHE 0.019 0.002 PHE D 22 TRP 0.002 0.001 TRP B 60 HIS 0.002 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 4440) covalent geometry : angle 0.61710 ( 6012) SS BOND : bond 0.00268 ( 6) SS BOND : angle 0.20399 ( 12) hydrogen bonds : bond 0.03429 ( 93) hydrogen bonds : angle 5.68017 ( 300) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.184 Fit side-chains REVERT: A 34 ASP cc_start: 0.8462 (m-30) cc_final: 0.8216 (m-30) REVERT: A 36 GLU cc_start: 0.8489 (tt0) cc_final: 0.8185 (tt0) REVERT: A 38 ASP cc_start: 0.8672 (p0) cc_final: 0.8225 (p0) REVERT: B 45 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7750 (mtm-85) REVERT: C 38 ASP cc_start: 0.8378 (p0) cc_final: 0.7933 (p0) REVERT: D 45 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7448 (ttm170) REVERT: E 16 GLU cc_start: 0.6410 (mp0) cc_final: 0.5999 (tp30) REVERT: E 53 ASP cc_start: 0.8030 (t0) cc_final: 0.7782 (t0) REVERT: F 69 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7419 (mp0) REVERT: F 89 GLN cc_start: 0.6166 (tt0) cc_final: 0.5735 (mt0) outliers start: 12 outliers final: 10 residues processed: 88 average time/residue: 0.0684 time to fit residues: 7.7404 Evaluate side-chains 81 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 55 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.131227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.109541 restraints weight = 6686.997| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 3.07 r_work: 0.3979 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4446 Z= 0.183 Angle : 0.665 6.234 6024 Z= 0.372 Chirality : 0.050 0.141 630 Planarity : 0.004 0.038 774 Dihedral : 5.944 28.541 573 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.25 % Allowed : 15.24 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 45 TYR 0.016 0.002 TYR F 26 PHE 0.020 0.003 PHE D 22 TRP 0.002 0.001 TRP C 60 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 4440) covalent geometry : angle 0.66524 ( 6012) SS BOND : bond 0.00350 ( 6) SS BOND : angle 0.31314 ( 12) hydrogen bonds : bond 0.03694 ( 93) hydrogen bonds : angle 5.75112 ( 300) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.196 Fit side-chains REVERT: A 34 ASP cc_start: 0.8422 (m-30) cc_final: 0.8173 (m-30) REVERT: A 36 GLU cc_start: 0.8436 (tt0) cc_final: 0.8133 (tt0) REVERT: A 38 ASP cc_start: 0.8705 (p0) cc_final: 0.8272 (p0) REVERT: B 45 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7789 (mtm-85) REVERT: C 38 ASP cc_start: 0.8464 (p0) cc_final: 0.8065 (p0) REVERT: E 16 GLU cc_start: 0.6761 (mp0) cc_final: 0.6142 (tp30) REVERT: F 69 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7600 (tm-30) REVERT: F 89 GLN cc_start: 0.6335 (tt0) cc_final: 0.5688 (mt0) outliers start: 16 outliers final: 12 residues processed: 86 average time/residue: 0.0746 time to fit residues: 8.2182 Evaluate side-chains 86 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 49 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 32 optimal weight: 0.2980 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS B 51 HIS E 51 HIS F 24 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.127397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.106521 restraints weight = 7528.904| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 3.06 r_work: 0.3919 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 4446 Z= 0.258 Angle : 0.735 6.168 6024 Z= 0.417 Chirality : 0.053 0.151 630 Planarity : 0.005 0.041 774 Dihedral : 6.399 31.408 573 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 3.86 % Allowed : 15.65 % Favored : 80.49 % 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 are not related in a simple way. whole: -3.64 (0.26), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.20), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 81 TYR 0.020 0.003 TYR F 26 PHE 0.021 0.003 PHE D 22 TRP 0.003 0.001 TRP C 60 HIS 0.004 0.001 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00583 ( 4440) covalent geometry : angle 0.73502 ( 6012) SS BOND : bond 0.00530 ( 6) SS BOND : angle 0.47242 ( 12) hydrogen bonds : bond 0.04322 ( 93) hydrogen bonds : angle 5.94500 ( 300) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.177 Fit side-chains REVERT: A 34 ASP cc_start: 0.8370 (m-30) cc_final: 0.8107 (m-30) REVERT: A 36 GLU cc_start: 0.8456 (tt0) cc_final: 0.8181 (tt0) REVERT: A 38 ASP cc_start: 0.8737 (p0) cc_final: 0.8392 (p0) REVERT: B 81 ARG cc_start: 0.7868 (ttm110) cc_final: 0.7513 (mtm180) REVERT: C 38 ASP cc_start: 0.8521 (p0) cc_final: 0.8237 (p0) REVERT: D 39 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8197 (tp) REVERT: E 16 GLU cc_start: 0.6789 (mp0) cc_final: 0.6091 (tp30) REVERT: F 89 GLN cc_start: 0.6227 (tt0) cc_final: 0.5535 (mt0) outliers start: 19 outliers final: 16 residues processed: 90 average time/residue: 0.0574 time to fit residues: 6.8502 Evaluate side-chains 91 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 68 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 3 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.125195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.104007 restraints weight = 7264.702| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 3.02 r_work: 0.3901 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 4446 Z= 0.282 Angle : 0.762 5.703 6024 Z= 0.434 Chirality : 0.054 0.154 630 Planarity : 0.005 0.041 774 Dihedral : 6.543 31.815 573 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 4.67 % Allowed : 15.45 % Favored : 79.88 % 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 are not related in a simple way. whole: -3.91 (0.25), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.19), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 81 TYR 0.020 0.003 TYR F 26 PHE 0.024 0.003 PHE D 22 TRP 0.002 0.001 TRP C 60 HIS 0.005 0.001 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00638 ( 4440) covalent geometry : angle 0.76229 ( 6012) SS BOND : bond 0.00642 ( 6) SS BOND : angle 0.44530 ( 12) hydrogen bonds : bond 0.04408 ( 93) hydrogen bonds : angle 5.97426 ( 300) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.201 Fit side-chains REVERT: A 28 SER cc_start: 0.9064 (t) cc_final: 0.8783 (p) REVERT: A 34 ASP cc_start: 0.8386 (m-30) cc_final: 0.8125 (m-30) REVERT: A 38 ASP cc_start: 0.8746 (p0) cc_final: 0.8527 (p0) REVERT: B 45 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7921 (mtm-85) REVERT: B 81 ARG cc_start: 0.7931 (ttm110) cc_final: 0.7576 (mtm180) REVERT: C 38 ASP cc_start: 0.8523 (p0) cc_final: 0.8216 (p0) REVERT: D 6 MET cc_start: 0.5727 (ttm) cc_final: 0.5455 (ttm) REVERT: D 39 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8189 (tp) REVERT: E 16 GLU cc_start: 0.6843 (mp0) cc_final: 0.6108 (tp30) REVERT: F 76 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8477 (m-30) REVERT: F 89 GLN cc_start: 0.6080 (tt0) cc_final: 0.5321 (mt0) outliers start: 23 outliers final: 17 residues processed: 95 average time/residue: 0.0598 time to fit residues: 7.5499 Evaluate side-chains 99 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 76 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.0770 chunk 12 optimal weight: 6.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.131454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.109191 restraints weight = 6788.269| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 3.17 r_work: 0.3955 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4446 Z= 0.157 Angle : 0.666 5.844 6024 Z= 0.373 Chirality : 0.049 0.141 630 Planarity : 0.004 0.039 774 Dihedral : 6.042 27.037 573 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.27 % Allowed : 15.85 % Favored : 79.88 % 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 are not related in a simple way. whole: -3.79 (0.26), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.20), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 81 TYR 0.013 0.002 TYR D 63 PHE 0.027 0.002 PHE E 70 TRP 0.002 0.001 TRP A 60 HIS 0.003 0.001 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 4440) covalent geometry : angle 0.66691 ( 6012) SS BOND : bond 0.00423 ( 6) SS BOND : angle 0.24245 ( 12) hydrogen bonds : bond 0.03441 ( 93) hydrogen bonds : angle 5.76469 ( 300) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.109 Fit side-chains REVERT: A 28 SER cc_start: 0.9006 (t) cc_final: 0.8755 (p) REVERT: A 34 ASP cc_start: 0.8433 (m-30) cc_final: 0.8206 (m-30) REVERT: A 38 ASP cc_start: 0.8664 (p0) cc_final: 0.8313 (p0) REVERT: A 40 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9082 (tt) REVERT: B 45 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7923 (mtm-85) REVERT: B 81 ARG cc_start: 0.7966 (ttm110) cc_final: 0.7618 (mtm180) REVERT: C 38 ASP cc_start: 0.8406 (p0) cc_final: 0.8003 (p0) REVERT: D 6 MET cc_start: 0.5832 (ttm) cc_final: 0.5579 (ttm) REVERT: E 16 GLU cc_start: 0.6691 (mp0) cc_final: 0.5851 (tp30) REVERT: F 28 SER cc_start: 0.9033 (p) cc_final: 0.8746 (t) REVERT: F 69 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7311 (tm-30) REVERT: F 89 GLN cc_start: 0.6133 (tt0) cc_final: 0.5434 (mt0) outliers start: 21 outliers final: 15 residues processed: 97 average time/residue: 0.0607 time to fit residues: 7.6780 Evaluate side-chains 98 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain F residue 6 MET Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 68 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 9 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.133037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.110644 restraints weight = 6774.759| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 3.18 r_work: 0.3981 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4446 Z= 0.139 Angle : 0.654 7.366 6024 Z= 0.364 Chirality : 0.049 0.153 630 Planarity : 0.004 0.039 774 Dihedral : 5.868 25.392 573 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.46 % Allowed : 17.07 % Favored : 79.47 % 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 are not related in a simple way. whole: -3.72 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.20), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 81 TYR 0.012 0.002 TYR B 10 PHE 0.027 0.002 PHE C 22 TRP 0.003 0.001 TRP A 60 HIS 0.002 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4440) covalent geometry : angle 0.65497 ( 6012) SS BOND : bond 0.00363 ( 6) SS BOND : angle 0.31635 ( 12) hydrogen bonds : bond 0.03253 ( 93) hydrogen bonds : angle 5.61965 ( 300) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.175 Fit side-chains REVERT: A 28 SER cc_start: 0.9022 (t) cc_final: 0.8755 (p) REVERT: A 34 ASP cc_start: 0.8453 (m-30) cc_final: 0.8206 (m-30) REVERT: A 38 ASP cc_start: 0.8629 (p0) cc_final: 0.8342 (p0) REVERT: A 40 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9047 (tt) REVERT: B 45 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7926 (mtm-85) REVERT: B 81 ARG cc_start: 0.7915 (ttm110) cc_final: 0.7582 (mtm180) REVERT: C 38 ASP cc_start: 0.8412 (p0) cc_final: 0.8019 (p0) REVERT: D 6 MET cc_start: 0.5762 (ttm) cc_final: 0.5505 (ttm) REVERT: E 16 GLU cc_start: 0.6618 (mp0) cc_final: 0.5928 (tp30) REVERT: F 28 SER cc_start: 0.9007 (p) cc_final: 0.8715 (t) REVERT: F 89 GLN cc_start: 0.6192 (tt0) cc_final: 0.5460 (mt0) outliers start: 17 outliers final: 13 residues processed: 96 average time/residue: 0.0450 time to fit residues: 5.7400 Evaluate side-chains 96 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain F residue 6 MET Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 17 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 9 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.129891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.107492 restraints weight = 6912.164| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 3.15 r_work: 0.3935 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4446 Z= 0.207 Angle : 0.707 7.161 6024 Z= 0.398 Chirality : 0.051 0.167 630 Planarity : 0.004 0.039 774 Dihedral : 6.144 29.341 573 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 3.25 % Allowed : 16.67 % Favored : 80.08 % 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 are not related in a simple way. whole: -3.79 (0.26), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.20), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 81 TYR 0.015 0.002 TYR D 63 PHE 0.022 0.003 PHE D 22 TRP 0.002 0.001 TRP A 60 HIS 0.003 0.001 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 4440) covalent geometry : angle 0.70720 ( 6012) SS BOND : bond 0.00489 ( 6) SS BOND : angle 0.38492 ( 12) hydrogen bonds : bond 0.03748 ( 93) hydrogen bonds : angle 5.67615 ( 300) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.179 Fit side-chains REVERT: A 28 SER cc_start: 0.9028 (t) cc_final: 0.8718 (p) REVERT: A 34 ASP cc_start: 0.8480 (m-30) cc_final: 0.8250 (m-30) REVERT: A 38 ASP cc_start: 0.8657 (p0) cc_final: 0.8358 (p0) REVERT: A 40 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9112 (tt) REVERT: B 45 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7936 (mtm-85) REVERT: B 81 ARG cc_start: 0.7948 (ttm110) cc_final: 0.7597 (mtm180) REVERT: C 38 ASP cc_start: 0.8510 (p0) cc_final: 0.8128 (p0) REVERT: C 40 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.9018 (tt) REVERT: D 6 MET cc_start: 0.5747 (ttm) cc_final: 0.5494 (ttm) REVERT: D 89 GLN cc_start: 0.6452 (tt0) cc_final: 0.6226 (tt0) REVERT: F 89 GLN cc_start: 0.6115 (tt0) cc_final: 0.5398 (mt0) outliers start: 16 outliers final: 13 residues processed: 92 average time/residue: 0.0604 time to fit residues: 7.3825 Evaluate side-chains 95 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain F residue 6 MET Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 7 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.130144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.107770 restraints weight = 6859.028| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 3.15 r_work: 0.3942 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4446 Z= 0.189 Angle : 0.704 7.120 6024 Z= 0.394 Chirality : 0.051 0.164 630 Planarity : 0.004 0.039 774 Dihedral : 6.115 28.576 573 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 3.46 % Allowed : 17.07 % Favored : 79.47 % 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 are not related in a simple way. whole: -3.81 (0.26), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.20), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 81 TYR 0.015 0.002 TYR D 63 PHE 0.024 0.003 PHE C 22 TRP 0.002 0.000 TRP A 60 HIS 0.003 0.001 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 4440) covalent geometry : angle 0.70439 ( 6012) SS BOND : bond 0.00450 ( 6) SS BOND : angle 0.39423 ( 12) hydrogen bonds : bond 0.03569 ( 93) hydrogen bonds : angle 5.63334 ( 300) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 979.55 seconds wall clock time: 17 minutes 36.06 seconds (1056.06 seconds total)