Starting phenix.real_space_refine on Tue Feb 11 05:43:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a7p_15223/02_2025/8a7p_15223.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a7p_15223/02_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_15223/02_2025/8a7p_15223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a7p_15223/02_2025/8a7p_15223.map" model { file = "/net/cci-nas-00/data/ceres_data/8a7p_15223/02_2025/8a7p_15223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a7p_15223/02_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-5592/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: 4.48, per 1000 atoms: 1.04 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: 0.95 Conformation dependent library (CDL) restraints added in 507.4 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: 0.69 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: 1.17 Time building geometry restraints manager: 1.10 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: 3.320 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.060 Find NCS groups from input model: 0.160 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.700 ------------------------------------------------------------------------------- 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 : 0.472 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: 0.1872 time to fit residues: 28.5495 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 : 0.469 ------------------------------------------------------------------------------- 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: 8.9990 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 = 0.108575 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 : 0.518 Fit side-chains REVERT: A 36 GLU cc_start: 0.8438 (tt0) cc_final: 0.8170 (tt0) REVERT: A 38 ASP cc_start: 0.8732 (p0) cc_final: 0.8211 (p0) REVERT: A 40 LEU cc_start: 0.9245 (tp) cc_final: 0.8838 (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: 0.8243 (p0) REVERT: C 40 LEU cc_start: 0.9115 (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: 0.8296 (p0) cc_final: 0.8091 (p0) REVERT: D 89 GLN cc_start: 0.6901 (tt0) cc_final: 0.6061 (mt0) REVERT: E 50 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7595 (mp0) REVERT: E 74 GLU cc_start: 0.8136 (pm20) cc_final: 0.7794 (pm20) REVERT: F 89 GLN cc_start: 0.6260 (tt0) cc_final: 0.5890 (mt0) outliers start: 8 outliers final: 6 residues processed: 87 average time/residue: 0.1464 time to fit residues: 16.6714 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 : 0.476 ------------------------------------------------------------------------------- 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: 1.9990 chunk 23 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 25 optimal weight: 0.0070 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS D 84 HIS E 13 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.133575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.111559 restraints weight = 6637.061| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 3.08 r_work: 0.4003 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4440 Z= 0.263 Angle : 0.652 5.565 6012 Z= 0.368 Chirality : 0.049 0.142 630 Planarity : 0.005 0.045 774 Dihedral : 5.871 26.701 573 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.44 % Allowed : 14.63 % Favored : 82.93 % 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: -3.28 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 60 HIS 0.003 0.001 HIS F 84 PHE 0.020 0.003 PHE D 22 TYR 0.016 0.002 TYR F 26 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 : 0.539 Fit side-chains REVERT: A 36 GLU cc_start: 0.8487 (tt0) cc_final: 0.8167 (tt0) REVERT: A 38 ASP cc_start: 0.8698 (p0) cc_final: 0.8191 (p0) REVERT: B 45 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7425 (mtm180) REVERT: C 38 ASP cc_start: 0.8463 (p0) cc_final: 0.8017 (p0) REVERT: D 45 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7632 (ttm170) REVERT: E 42 ASN cc_start: 0.8667 (m110) cc_final: 0.8379 (m110) REVERT: E 50 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7526 (mp0) REVERT: F 69 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7500 (mp0) REVERT: F 89 GLN cc_start: 0.6315 (tt0) cc_final: 0.5803 (mt0) outliers start: 12 outliers final: 8 residues processed: 85 average time/residue: 0.1485 time to fit residues: 16.2749 Evaluate side-chains 80 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 19 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.129835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.108955 restraints weight = 7378.999| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 3.05 r_work: 0.3943 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 4440 Z= 0.363 Angle : 0.715 5.456 6012 Z= 0.409 Chirality : 0.052 0.152 630 Planarity : 0.005 0.045 774 Dihedral : 6.300 31.592 573 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.46 % Allowed : 15.85 % 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: -3.50 (0.26), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.20), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 60 HIS 0.004 0.001 HIS D 31 PHE 0.021 0.003 PHE D 22 TYR 0.022 0.003 TYR F 26 ARG 0.003 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 97 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.469 Fit side-chains REVERT: A 36 GLU cc_start: 0.8462 (tt0) cc_final: 0.8168 (tt0) REVERT: A 38 ASP cc_start: 0.8769 (p0) cc_final: 0.8321 (p0) REVERT: A 40 LEU cc_start: 0.9289 (tp) cc_final: 0.9072 (tt) REVERT: B 45 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7828 (mtm-85) REVERT: C 38 ASP cc_start: 0.8497 (p0) cc_final: 0.8099 (p0) REVERT: E 42 ASN cc_start: 0.8805 (m110) cc_final: 0.8450 (m110) REVERT: F 89 GLN cc_start: 0.6355 (tt0) cc_final: 0.5785 (mt0) outliers start: 17 outliers final: 14 residues processed: 89 average time/residue: 0.1493 time to fit residues: 17.0121 Evaluate side-chains 89 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 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 38 ASP 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 68 THR 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: 0.0370 chunk 28 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.8062 ------------------------------------------------------------------------------- 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 = 0.4297 r_free = 0.4297 target = 0.126553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.104706 restraints weight = 7397.137| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 3.38 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: 0.7689 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4440 Z= 0.174 Angle : 0.617 6.357 6012 Z= 0.341 Chirality : 0.048 0.135 630 Planarity : 0.004 0.039 774 Dihedral : 5.747 25.126 573 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.64 % Allowed : 16.26 % Favored : 81.10 % 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: -3.49 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (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 0.021 0.002 PHE E 70 TYR 0.013 0.002 TYR B 10 ARG 0.010 0.000 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 88 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.491 Fit side-chains REVERT: A 36 GLU cc_start: 0.8500 (tt0) cc_final: 0.8201 (tt0) REVERT: A 38 ASP cc_start: 0.8631 (p0) cc_final: 0.8228 (p0) REVERT: A 40 LEU cc_start: 0.9118 (tp) cc_final: 0.8836 (tt) REVERT: B 45 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7762 (mtm-85) REVERT: B 81 ARG cc_start: 0.7888 (ttm110) cc_final: 0.7593 (mtm180) REVERT: C 38 ASP cc_start: 0.8373 (p0) cc_final: 0.7951 (p0) REVERT: D 45 ARG cc_start: 0.7804 (ttm170) cc_final: 0.7096 (mtt180) REVERT: E 22 PHE cc_start: 0.7858 (p90) cc_final: 0.7441 (p90) REVERT: E 42 ASN cc_start: 0.8540 (m110) cc_final: 0.8267 (m110) REVERT: F 28 SER cc_start: 0.8968 (p) cc_final: 0.8740 (t) REVERT: F 69 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7272 (mp0) REVERT: F 89 GLN cc_start: 0.6244 (tt0) cc_final: 0.5572 (mt0) outliers start: 13 outliers final: 9 residues processed: 84 average time/residue: 0.1391 time to fit residues: 15.2834 Evaluate side-chains 83 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 49 VAL Chi-restraints excluded: chain D residue 68 THR 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: 2.9990 chunk 38 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 43 optimal weight: 0.0770 chunk 31 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 2.4144 ------------------------------------------------------------------------------- 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 = 0.4407 r_free = 0.4407 target = 0.132757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.111125 restraints weight = 6721.943| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 3.12 r_work: 0.4006 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4440 Z= 0.204 Angle : 0.623 5.426 6012 Z= 0.347 Chirality : 0.048 0.141 630 Planarity : 0.004 0.037 774 Dihedral : 5.697 25.679 573 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.46 % Allowed : 15.45 % Favored : 81.10 % 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: -3.52 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 60 HIS 0.002 0.001 HIS B 31 PHE 0.020 0.002 PHE A 70 TYR 0.011 0.002 TYR B 10 ARG 0.006 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 97 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.523 Fit side-chains REVERT: A 36 GLU cc_start: 0.8433 (tt0) cc_final: 0.8127 (tt0) REVERT: A 38 ASP cc_start: 0.8650 (p0) cc_final: 0.8266 (p0) REVERT: A 40 LEU cc_start: 0.9200 (tp) cc_final: 0.8983 (tt) REVERT: B 45 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7881 (mtm-85) REVERT: B 81 ARG cc_start: 0.7822 (ttm110) cc_final: 0.7501 (mtm180) REVERT: C 38 ASP cc_start: 0.8405 (p0) cc_final: 0.8046 (p0) REVERT: D 39 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8051 (tp) REVERT: D 45 ARG cc_start: 0.7947 (ttm170) cc_final: 0.7262 (mtt180) REVERT: E 22 PHE cc_start: 0.7908 (p90) cc_final: 0.7610 (p90) REVERT: E 42 ASN cc_start: 0.8662 (m110) cc_final: 0.8382 (m110) REVERT: F 69 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7452 (mp0) REVERT: F 89 GLN cc_start: 0.6364 (tt0) cc_final: 0.5678 (mt0) outliers start: 17 outliers final: 14 residues processed: 90 average time/residue: 0.1334 time to fit residues: 15.8741 Evaluate side-chains 90 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER 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 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 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 37 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 13 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- 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 = 0.4369 r_free = 0.4369 target = 0.130882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.109898 restraints weight = 7174.992| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 3.04 r_work: 0.3970 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4440 Z= 0.272 Angle : 0.660 6.937 6012 Z= 0.370 Chirality : 0.050 0.144 630 Planarity : 0.004 0.037 774 Dihedral : 5.945 28.482 573 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % 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 (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: -3.65 (0.26), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (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 D 22 TYR 0.014 0.002 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 98 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.475 Fit side-chains REVERT: A 36 GLU cc_start: 0.8455 (tt0) cc_final: 0.8170 (tt0) REVERT: A 38 ASP cc_start: 0.8682 (p0) cc_final: 0.8300 (p0) REVERT: A 40 LEU cc_start: 0.9199 (tp) cc_final: 0.8920 (tt) REVERT: B 81 ARG cc_start: 0.7877 (ttm110) cc_final: 0.7551 (mtm180) REVERT: C 38 ASP cc_start: 0.8461 (p0) cc_final: 0.8082 (p0) REVERT: D 39 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8040 (tp) REVERT: D 45 ARG cc_start: 0.7910 (ttm170) cc_final: 0.7177 (mtt180) REVERT: E 42 ASN cc_start: 0.8622 (m110) cc_final: 0.8284 (m110) REVERT: F 69 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7398 (mp0) REVERT: F 89 GLN cc_start: 0.6225 (tt0) cc_final: 0.5535 (mt0) outliers start: 19 outliers final: 17 residues processed: 89 average time/residue: 0.1375 time to fit residues: 15.9313 Evaluate side-chains 94 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 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 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: 6.9990 chunk 30 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 51 HIS B 51 HIS C 51 HIS F 24 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.125177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.104008 restraints weight = 7125.081| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 3.03 r_work: 0.3894 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 : 0.006 0.047 4440 Z= 0.419 Angle : 0.751 6.523 6012 Z= 0.427 Chirality : 0.054 0.154 630 Planarity : 0.005 0.039 774 Dihedral : 6.489 31.457 573 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 3.66 % Allowed : 16.06 % Favored : 80.28 % 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: -3.90 (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 TRP 0.003 0.001 TRP A 60 HIS 0.005 0.001 HIS B 31 PHE 0.022 0.003 PHE A 70 TYR 0.021 0.003 TYR D 26 ARG 0.004 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 98 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.492 Fit side-chains REVERT: A 38 ASP cc_start: 0.8723 (p0) cc_final: 0.8316 (p0) REVERT: B 34 ASP cc_start: 0.8245 (m-30) cc_final: 0.7403 (t70) REVERT: C 38 ASP cc_start: 0.8517 (p0) cc_final: 0.8096 (p0) REVERT: D 39 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8160 (tp) REVERT: D 41 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8121 (tttm) REVERT: E 42 ASN cc_start: 0.8700 (m110) cc_final: 0.8190 (m110) REVERT: F 69 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7403 (mp0) REVERT: F 89 GLN cc_start: 0.6091 (tt0) cc_final: 0.5379 (mt0) outliers start: 18 outliers final: 16 residues processed: 90 average time/residue: 0.1505 time to fit residues: 17.6383 Evaluate side-chains 95 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 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 41 LYS 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 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: 2.9990 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.4423 r_free = 0.4423 target = 0.134515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.113699 restraints weight = 7168.039| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 3.14 r_work: 0.4034 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4440 Z= 0.156 Angle : 0.625 6.299 6012 Z= 0.343 Chirality : 0.047 0.133 630 Planarity : 0.004 0.060 774 Dihedral : 5.631 22.831 573 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.85 % Allowed : 18.29 % 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: -3.74 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.20), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 60 HIS 0.002 0.000 HIS B 31 PHE 0.019 0.002 PHE C 22 TYR 0.013 0.001 TYR B 10 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 99 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.466 Fit side-chains REVERT: A 28 SER cc_start: 0.8921 (t) cc_final: 0.8584 (p) REVERT: A 38 ASP cc_start: 0.8516 (p0) cc_final: 0.8250 (p0) REVERT: A 40 LEU cc_start: 0.9195 (tp) cc_final: 0.8969 (tt) REVERT: B 34 ASP cc_start: 0.8270 (m-30) cc_final: 0.7483 (t70) REVERT: B 81 ARG cc_start: 0.8001 (ttm110) cc_final: 0.7559 (mtm180) REVERT: C 16 GLU cc_start: 0.7165 (mp0) cc_final: 0.6128 (tm-30) REVERT: C 28 SER cc_start: 0.9006 (t) cc_final: 0.8785 (p) REVERT: C 38 ASP cc_start: 0.8344 (p0) cc_final: 0.7933 (p0) REVERT: D 67 TYR cc_start: 0.8606 (m-80) cc_final: 0.8371 (m-80) REVERT: E 16 GLU cc_start: 0.7458 (mp0) cc_final: 0.5996 (tp30) REVERT: E 42 ASN cc_start: 0.8548 (m110) cc_final: 0.8239 (m-40) REVERT: F 69 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7398 (mp0) REVERT: F 89 GLN cc_start: 0.6325 (tt0) cc_final: 0.5542 (mt0) outliers start: 14 outliers final: 10 residues processed: 94 average time/residue: 0.1506 time to fit residues: 18.2794 Evaluate side-chains 89 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER 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 38 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 68 THR 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: 10.0000 chunk 8 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.4307 r_free = 0.4307 target = 0.127068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.104874 restraints weight = 7288.729| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 3.33 r_work: 0.4025 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4440 Z= 0.174 Angle : 0.634 7.042 6012 Z= 0.348 Chirality : 0.047 0.132 630 Planarity : 0.004 0.052 774 Dihedral : 5.564 23.375 573 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 2.64 % Allowed : 19.51 % Favored : 77.85 % 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: -3.68 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 60 HIS 0.002 0.000 HIS B 31 PHE 0.020 0.002 PHE C 22 TYR 0.012 0.002 TYR B 10 ARG 0.012 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 97 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.525 Fit side-chains REVERT: A 28 SER cc_start: 0.8895 (t) cc_final: 0.8541 (p) REVERT: A 38 ASP cc_start: 0.8535 (p0) cc_final: 0.8322 (p0) REVERT: B 34 ASP cc_start: 0.8234 (m-30) cc_final: 0.7489 (t70) REVERT: B 45 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7551 (mtm-85) REVERT: B 81 ARG cc_start: 0.8024 (ttm110) cc_final: 0.7580 (mtm180) REVERT: C 38 ASP cc_start: 0.8342 (p0) cc_final: 0.7949 (p0) REVERT: C 53 ASP cc_start: 0.8188 (t0) cc_final: 0.7988 (t0) REVERT: D 67 TYR cc_start: 0.8500 (m-80) cc_final: 0.8201 (m-80) REVERT: E 16 GLU cc_start: 0.7229 (mp0) cc_final: 0.5859 (tp30) REVERT: E 42 ASN cc_start: 0.8424 (m110) cc_final: 0.8080 (m-40) REVERT: F 69 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7290 (mp0) REVERT: F 89 GLN cc_start: 0.6212 (tt0) cc_final: 0.5439 (mt0) outliers start: 13 outliers final: 10 residues processed: 92 average time/residue: 0.1443 time to fit residues: 17.1872 Evaluate side-chains 90 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER 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 38 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 68 THR 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: 9.9990 chunk 5 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.4301 r_free = 0.4301 target = 0.125287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.104674 restraints weight = 7618.891| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 3.06 r_work: 0.3883 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 4440 Z= 0.477 Angle : 0.812 7.090 6012 Z= 0.457 Chirality : 0.056 0.161 630 Planarity : 0.005 0.038 774 Dihedral : 6.533 33.609 573 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 3.25 % Allowed : 17.28 % 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: -3.99 (0.25), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.19), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 60 HIS 0.005 0.002 HIS D 31 PHE 0.025 0.004 PHE D 22 TYR 0.021 0.003 TYR F 26 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: 1957.40 seconds wall clock time: 35 minutes 37.44 seconds (2137.44 seconds total)