Starting phenix.real_space_refine on Thu Mar 6 01:06:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a7p_15223/03_2025/8a7p_15223.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a7p_15223/03_2025/8a7p_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_15223/03_2025/8a7p_15223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a7p_15223/03_2025/8a7p_15223.map" model { file = "/net/cci-nas-00/data/ceres_data/8a7p_15223/03_2025/8a7p_15223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a7p_15223/03_2025/8a7p_15223.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.74, per 1000 atoms: 1.10 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: 0.89 Conformation dependent library (CDL) restraints added in 494.0 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: 0.75 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: 1.19 Time building geometry restraints manager: 1.13 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: 0.02 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: 4.720 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.700 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.000 ------------------------------------------------------------------------------- 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 4440 Z= 0.141 Angle : 0.545 3.765 6012 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (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 TRP 0.001 0.000 TRP B 60 HIS 0.003 0.001 HIS F 31 PHE 0.012 0.002 PHE A 22 TYR 0.006 0.001 TYR D 63 ARG 0.002 0.000 ARG E 12 *********************** 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 : 0.448 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: 0.6042 (mt0) REVERT: E 53 ASP cc_start: 0.7896 (t0) cc_final: 0.7665 (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: 0.1865 time to fit residues: 28.5277 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 : 0.481 ------------------------------------------------------------------------------- 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 40 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 0.0770 chunk 28 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- 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 E 31 HIS E 84 HIS E 89 GLN F 31 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.131426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.108576 restraints weight = 7301.704| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 3.33 r_work: 0.4043 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4440 Z= 0.264 Angle : 0.683 5.776 6012 Z= 0.382 Chirality : 0.049 0.152 630 Planarity : 0.005 0.050 774 Dihedral : 5.665 29.227 573 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.63 % Allowed : 11.18 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.28), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 60 HIS 0.005 0.001 HIS B 31 PHE 0.021 0.003 PHE D 22 TYR 0.014 0.002 TYR D 26 ARG 0.002 0.000 ARG B 45 *********************** 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 88 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.486 Fit side-chains REVERT: A 36 GLU cc_start: 0.8439 (tt0) cc_final: 0.8172 (tt0) REVERT: A 38 ASP cc_start: 0.8733 (p0) cc_final: 0.8211 (p0) REVERT: A 40 LEU cc_start: 0.9245 (tp) cc_final: 0.8839 (tt) REVERT: B 20 SER cc_start: 0.8851 (p) cc_final: 0.8634 (p) REVERT: B 45 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7803 (mtm-85) REVERT: B 89 GLN cc_start: 0.6767 (tt0) cc_final: 0.6048 (mt0) REVERT: C 38 ASP cc_start: 0.8532 (p0) cc_final: 0.8242 (p0) REVERT: C 40 LEU cc_start: 0.9116 (tp) cc_final: 0.8882 (tp) REVERT: C 50 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7743 (mp0) REVERT: D 38 ASP cc_start: 0.8297 (p0) cc_final: 0.8091 (p0) REVERT: D 89 GLN cc_start: 0.6901 (tt0) cc_final: 0.6062 (mt0) REVERT: E 50 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7594 (mp0) REVERT: E 74 GLU cc_start: 0.8136 (pm20) cc_final: 0.7793 (pm20) REVERT: F 89 GLN cc_start: 0.6261 (tt0) cc_final: 0.5890 (mt0) outliers start: 8 outliers final: 6 residues processed: 87 average time/residue: 0.1447 time to fit residues: 16.4073 Evaluate side-chains 76 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 VAL 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 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 14 optimal weight: 5.9990 chunk 36 optimal weight: 0.4980 chunk 23 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 25 optimal weight: 0.0070 overall best weight: 2.1004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 HIS E 13 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.130315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.107614 restraints weight = 7086.849| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 3.37 r_work: 0.4053 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4440 Z= 0.184 Angle : 0.599 5.745 6012 Z= 0.333 Chirality : 0.047 0.137 630 Planarity : 0.004 0.044 774 Dihedral : 5.497 24.471 573 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.44 % Allowed : 14.02 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (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 TRP 0.002 0.001 TRP F 60 HIS 0.002 0.001 HIS F 84 PHE 0.019 0.002 PHE D 22 TYR 0.013 0.002 TYR E 67 ARG 0.002 0.000 ARG B 45 *********************** 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 87 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.523 Fit side-chains REVERT: A 36 GLU cc_start: 0.8500 (tt0) cc_final: 0.8189 (tt0) REVERT: A 38 ASP cc_start: 0.8642 (p0) cc_final: 0.8107 (p0) REVERT: A 40 LEU cc_start: 0.9144 (tp) cc_final: 0.8680 (tt) REVERT: B 45 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7775 (mtm-85) REVERT: B 89 GLN cc_start: 0.6735 (tt0) cc_final: 0.5897 (mt0) REVERT: C 38 ASP cc_start: 0.8405 (p0) cc_final: 0.7906 (p0) REVERT: C 40 LEU cc_start: 0.9053 (tp) cc_final: 0.8841 (tp) REVERT: C 50 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7563 (mp0) REVERT: D 45 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7406 (ttm170) REVERT: E 42 ASN cc_start: 0.8452 (m110) cc_final: 0.8183 (m110) REVERT: E 50 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7495 (mp0) REVERT: E 74 GLU cc_start: 0.8134 (pm20) cc_final: 0.7757 (pm20) REVERT: F 89 GLN cc_start: 0.6228 (tt0) cc_final: 0.5791 (mt0) outliers start: 12 outliers final: 9 residues processed: 85 average time/residue: 0.1720 time to fit residues: 19.3625 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 : 0.517 ------------------------------------------------------------------------------- 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 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 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 13 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 51 HIS B 51 HIS C 13 HIS C 51 HIS E 51 HIS F 24 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.127056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.106058 restraints weight = 7431.410| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 3.04 r_work: 0.3907 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 4440 Z= 0.488 Angle : 0.787 5.243 6012 Z= 0.454 Chirality : 0.055 0.159 630 Planarity : 0.006 0.049 774 Dihedral : 6.652 32.938 573 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 3.86 % Allowed : 14.23 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.26), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.20), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 60 HIS 0.006 0.002 HIS D 31 PHE 0.026 0.004 PHE A 30 TYR 0.028 0.004 TYR F 26 ARG 0.002 0.000 ARG B 45 *********************** 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 100 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.459 Fit side-chains REVERT: A 36 GLU cc_start: 0.8493 (tt0) cc_final: 0.8246 (tt0) REVERT: A 38 ASP cc_start: 0.8793 (p0) cc_final: 0.8568 (p0) REVERT: B 45 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7914 (mtm-85) REVERT: C 38 ASP cc_start: 0.8613 (p0) cc_final: 0.8337 (p0) REVERT: F 89 GLN cc_start: 0.6388 (tt0) cc_final: 0.5753 (mt0) outliers start: 19 outliers final: 17 residues processed: 92 average time/residue: 0.1775 time to fit residues: 21.2245 Evaluate side-chains 90 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 38 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 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 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 55 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 41 optimal weight: 0.0470 chunk 15 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.130461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.109737 restraints weight = 7239.791| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 3.05 r_work: 0.3969 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4440 Z= 0.265 Angle : 0.666 6.330 6012 Z= 0.374 Chirality : 0.050 0.142 630 Planarity : 0.004 0.042 774 Dihedral : 6.082 28.105 573 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.25 % Allowed : 16.06 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.26), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.20), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 60 HIS 0.003 0.001 HIS B 31 PHE 0.021 0.003 PHE E 70 TYR 0.014 0.002 TYR F 26 ARG 0.010 0.001 ARG B 81 *********************** 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 92 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.590 Fit side-chains REVERT: A 36 GLU cc_start: 0.8475 (tt0) cc_final: 0.8172 (tt0) REVERT: A 38 ASP cc_start: 0.8681 (p0) cc_final: 0.8230 (p0) REVERT: A 40 LEU cc_start: 0.9200 (tp) cc_final: 0.8919 (tt) REVERT: B 45 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7769 (mtm-85) REVERT: B 81 ARG cc_start: 0.7866 (ttm110) cc_final: 0.7545 (mtm180) REVERT: C 38 ASP cc_start: 0.8426 (p0) cc_final: 0.8004 (p0) REVERT: F 69 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7351 (mp0) REVERT: F 89 GLN cc_start: 0.6361 (tt0) cc_final: 0.5651 (mt0) outliers start: 16 outliers final: 12 residues processed: 86 average time/residue: 0.1641 time to fit residues: 18.5603 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 : 0.563 ------------------------------------------------------------------------------- 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 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 49 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 76 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 chunk 31 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.134483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.113439 restraints weight = 7133.432| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 3.17 r_work: 0.4026 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4440 Z= 0.171 Angle : 0.600 5.456 6012 Z= 0.332 Chirality : 0.047 0.133 630 Planarity : 0.004 0.038 774 Dihedral : 5.617 23.929 573 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.44 % Allowed : 16.67 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 60 HIS 0.002 0.000 HIS B 31 PHE 0.019 0.002 PHE C 22 TYR 0.013 0.002 TYR B 10 ARG 0.007 0.000 ARG B 81 *********************** 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 92 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.490 Fit side-chains REVERT: A 36 GLU cc_start: 0.8428 (tt0) cc_final: 0.8122 (tt0) REVERT: A 38 ASP cc_start: 0.8591 (p0) cc_final: 0.8211 (p0) REVERT: A 40 LEU cc_start: 0.9179 (tp) cc_final: 0.8919 (tt) REVERT: B 45 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7867 (mtm-85) REVERT: B 81 ARG cc_start: 0.7813 (ttm110) cc_final: 0.7514 (mtm180) REVERT: C 38 ASP cc_start: 0.8409 (p0) cc_final: 0.8050 (p0) REVERT: D 45 ARG cc_start: 0.7935 (ttm170) cc_final: 0.7242 (mtt180) REVERT: E 22 PHE cc_start: 0.7923 (p90) cc_final: 0.7677 (p90) REVERT: F 69 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7484 (mp0) REVERT: F 89 GLN cc_start: 0.6364 (tt0) cc_final: 0.5692 (mt0) outliers start: 12 outliers final: 11 residues processed: 87 average time/residue: 0.1506 time to fit residues: 17.3415 Evaluate side-chains 84 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 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 49 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 37 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- 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 = 0.4325 r_free = 0.4325 target = 0.126802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.106052 restraints weight = 7282.159| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 3.04 r_work: 0.3930 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 4440 Z= 0.362 Angle : 0.713 4.963 6012 Z= 0.405 Chirality : 0.052 0.151 630 Planarity : 0.005 0.039 774 Dihedral : 6.261 31.493 573 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.26), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.20), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 60 HIS 0.004 0.001 HIS B 31 PHE 0.022 0.003 PHE A 70 TYR 0.017 0.003 TYR F 26 ARG 0.006 0.000 ARG B 81 *********************** 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 94 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.465 Fit side-chains REVERT: A 36 GLU cc_start: 0.8407 (tt0) cc_final: 0.8091 (tt0) REVERT: A 38 ASP cc_start: 0.8725 (p0) cc_final: 0.8309 (p0) REVERT: B 34 ASP cc_start: 0.8291 (m-30) cc_final: 0.7456 (t70) REVERT: B 45 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7911 (mtm-85) REVERT: B 81 ARG cc_start: 0.7870 (ttm110) cc_final: 0.7519 (mtm180) REVERT: C 38 ASP cc_start: 0.8470 (p0) cc_final: 0.8087 (p0) REVERT: D 39 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8119 (tp) REVERT: F 69 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7482 (mp0) REVERT: F 89 GLN cc_start: 0.6290 (tt0) cc_final: 0.5542 (mt0) outliers start: 17 outliers final: 15 residues processed: 85 average time/residue: 0.1302 time to fit residues: 14.6714 Evaluate side-chains 93 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 27 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.128351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.106130 restraints weight = 6888.160| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 3.11 r_work: 0.3908 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 4440 Z= 0.379 Angle : 0.731 5.666 6012 Z= 0.415 Chirality : 0.053 0.151 630 Planarity : 0.005 0.041 774 Dihedral : 6.420 31.282 573 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.46 % Allowed : 17.48 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.26), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.19), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 60 HIS 0.004 0.001 HIS D 31 PHE 0.024 0.003 PHE D 22 TYR 0.017 0.003 TYR D 26 ARG 0.005 0.000 ARG B 81 *********************** 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 100 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.490 Fit side-chains REVERT: A 28 SER cc_start: 0.9058 (t) cc_final: 0.8746 (p) REVERT: A 38 ASP cc_start: 0.8732 (p0) cc_final: 0.8310 (p0) REVERT: B 34 ASP cc_start: 0.8258 (m-30) cc_final: 0.7380 (t70) REVERT: B 45 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7928 (mtm-85) REVERT: C 38 ASP cc_start: 0.8502 (p0) cc_final: 0.8114 (p0) REVERT: C 53 ASP cc_start: 0.8309 (t0) cc_final: 0.8101 (t0) REVERT: D 39 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8217 (tp) REVERT: F 69 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7460 (mp0) REVERT: F 89 GLN cc_start: 0.6169 (tt0) cc_final: 0.5429 (mt0) outliers start: 17 outliers final: 15 residues processed: 91 average time/residue: 0.1446 time to fit residues: 17.2005 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 : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 27 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.4404 r_free = 0.4404 target = 0.130376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.108115 restraints weight = 6858.112| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 3.16 r_work: 0.3945 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4440 Z= 0.266 Angle : 0.684 7.036 6012 Z= 0.382 Chirality : 0.050 0.145 630 Planarity : 0.005 0.055 774 Dihedral : 6.136 28.380 573 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.27 % Allowed : 16.87 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.26), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.20), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 60 HIS 0.003 0.001 HIS B 31 PHE 0.020 0.002 PHE A 70 TYR 0.013 0.002 TYR F 63 ARG 0.014 0.001 ARG B 81 *********************** 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: 21 poor density : 83 time to evaluate : 0.532 Fit side-chains REVERT: A 28 SER cc_start: 0.9045 (t) cc_final: 0.8728 (p) REVERT: A 38 ASP cc_start: 0.8673 (p0) cc_final: 0.8321 (p0) REVERT: A 40 LEU cc_start: 0.9228 (tp) cc_final: 0.8984 (tt) REVERT: B 34 ASP cc_start: 0.8251 (m-30) cc_final: 0.7425 (t70) REVERT: B 45 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7938 (mtm-85) REVERT: B 81 ARG cc_start: 0.7986 (ttm110) cc_final: 0.7519 (mtp85) REVERT: C 38 ASP cc_start: 0.8453 (p0) cc_final: 0.8046 (p0) REVERT: C 53 ASP cc_start: 0.8308 (t0) cc_final: 0.8091 (t0) REVERT: D 39 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8137 (tp) REVERT: D 89 GLN cc_start: 0.6474 (tt0) cc_final: 0.6257 (tt0) REVERT: F 69 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7420 (mp0) REVERT: F 89 GLN cc_start: 0.6169 (tt0) cc_final: 0.5448 (mt0) outliers start: 21 outliers final: 15 residues processed: 96 average time/residue: 0.1494 time to fit residues: 18.4434 Evaluate side-chains 97 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 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 E residue 40 LEU 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 5 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 42 optimal weight: 0.0270 chunk 16 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- 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 = 0.4415 r_free = 0.4415 target = 0.131324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.109027 restraints weight = 6744.170| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 3.11 r_work: 0.3958 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4440 Z= 0.247 Angle : 0.680 6.832 6012 Z= 0.378 Chirality : 0.050 0.162 630 Planarity : 0.004 0.047 774 Dihedral : 6.034 27.306 573 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.25 % Allowed : 17.89 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.26), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.20), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 60 HIS 0.003 0.001 HIS D 31 PHE 0.029 0.002 PHE C 22 TYR 0.013 0.002 TYR D 63 ARG 0.013 0.001 ARG B 81 ********************** 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 : 0.497 Fit side-chains REVERT: A 28 SER cc_start: 0.9008 (t) cc_final: 0.8706 (p) REVERT: A 38 ASP cc_start: 0.8616 (p0) cc_final: 0.8309 (p0) REVERT: A 40 LEU cc_start: 0.9235 (tp) cc_final: 0.8981 (tt) REVERT: B 34 ASP cc_start: 0.8277 (m-30) cc_final: 0.7469 (t70) REVERT: B 45 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7947 (mtm-85) REVERT: B 81 ARG cc_start: 0.7955 (ttm110) cc_final: 0.7504 (mtp85) REVERT: C 16 GLU cc_start: 0.7440 (mp0) cc_final: 0.5760 (tm-30) REVERT: C 38 ASP cc_start: 0.8430 (p0) cc_final: 0.8035 (p0) REVERT: C 53 ASP cc_start: 0.8331 (t0) cc_final: 0.8095 (t0) REVERT: D 39 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8132 (tp) REVERT: E 16 GLU cc_start: 0.7177 (mp0) cc_final: 0.5932 (tp30) REVERT: F 69 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7452 (mp0) REVERT: F 89 GLN cc_start: 0.6235 (tt0) cc_final: 0.5476 (mt0) outliers start: 16 outliers final: 14 residues processed: 91 average time/residue: 0.1493 time to fit residues: 17.4529 Evaluate side-chains 97 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 68 THR Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain E residue 40 LEU 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 15 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.4375 r_free = 0.4375 target = 0.128505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.106436 restraints weight = 6890.016| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 3.06 r_work: 0.3920 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4440 Z= 0.344 Angle : 0.723 6.615 6012 Z= 0.407 Chirality : 0.052 0.178 630 Planarity : 0.005 0.040 774 Dihedral : 6.305 30.929 573 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 3.86 % Allowed : 16.87 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.26), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.20), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 60 HIS 0.004 0.001 HIS D 31 PHE 0.023 0.003 PHE D 22 TYR 0.016 0.003 TYR D 63 ARG 0.012 0.001 ARG B 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2228.06 seconds wall clock time: 40 minutes 5.23 seconds (2405.23 seconds total)