Starting phenix.real_space_refine on Wed Sep 17 03:15:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xwd_38733/09_2025/8xwd_38733.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xwd_38733/09_2025/8xwd_38733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xwd_38733/09_2025/8xwd_38733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xwd_38733/09_2025/8xwd_38733.map" model { file = "/net/cci-nas-00/data/ceres_data/8xwd_38733/09_2025/8xwd_38733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xwd_38733/09_2025/8xwd_38733.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1686 2.51 5 N 426 2.21 5 O 558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2670 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 412 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "D" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 412 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "E" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 412 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "A" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 412 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "F" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 412 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "B" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 412 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'KDH': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'KDH': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'KDH': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'KDH': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'KDH': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'KDH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.83, per 1000 atoms: 0.31 Number of scatterers: 2670 At special positions: 0 Unit cell: (97.11, 98.77, 31.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 558 8.00 N 426 7.00 C 1686 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.24 Conformation dependent library (CDL) restraints added in 65.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 612 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 46 through 56 removed outlier: 6.858A pdb=" N GLY C 47 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL E 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA C 53 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR E 54 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL C 55 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA E 56 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLY C 47 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N HIS F 50 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N VAL C 49 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N VAL F 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY C 51 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N THR F 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA C 53 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ALA F 56 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL C 55 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 69 through 71 removed outlier: 6.532A pdb=" N VAL C 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 75 through 77 removed outlier: 8.643A pdb=" N THR C 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL F 77 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 80 through 82 removed outlier: 6.499A pdb=" N LYS C 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 46 through 56 removed outlier: 6.831A pdb=" N VAL D 48 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N HIS D 50 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY A 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLU D 46 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N VAL B 49 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL D 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N GLY B 51 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N HIS D 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N ALA B 53 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N VAL D 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N VAL B 55 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N THR D 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 71 removed outlier: 6.538A pdb=" N VAL D 70 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 75 through 77 removed outlier: 8.656A pdb=" N THR D 75 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 77 " --> pdb=" O ALA D 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 80 through 82 removed outlier: 6.516A pdb=" N LYS D 80 " --> pdb=" O THR A 81 " (cutoff:3.500A) 20 hydrogen bonds defined for protein. 60 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.26 Time building geometry restraints manager: 0.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.27: 432 1.27 - 1.34: 384 1.34 - 1.41: 270 1.41 - 1.48: 444 1.48 - 1.55: 1170 Bond restraints: 2700 Sorted by residual: bond pdb=" CB VAL D 40 " pdb=" CG1 VAL D 40 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.91e+00 bond pdb=" CB VAL A 40 " pdb=" CG1 VAL A 40 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.91e+00 bond pdb=" CB VAL F 40 " pdb=" CG1 VAL F 40 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.90e+00 bond pdb=" CB VAL E 40 " pdb=" CG1 VAL E 40 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.80e+00 bond pdb=" CB VAL B 40 " pdb=" CG1 VAL B 40 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.80e+00 ... (remaining 2695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 2879 0.94 - 1.89: 524 1.89 - 2.83: 179 2.83 - 3.77: 71 3.77 - 4.71: 37 Bond angle restraints: 3690 Sorted by residual: angle pdb=" N GLY D 73 " pdb=" CA GLY D 73 " pdb=" C GLY D 73 " ideal model delta sigma weight residual 114.10 118.21 -4.11 1.51e+00 4.39e-01 7.42e+00 angle pdb=" N GLY C 73 " pdb=" CA GLY C 73 " pdb=" C GLY C 73 " ideal model delta sigma weight residual 114.10 118.21 -4.11 1.51e+00 4.39e-01 7.40e+00 angle pdb=" N GLY B 73 " pdb=" CA GLY B 73 " pdb=" C GLY B 73 " ideal model delta sigma weight residual 114.10 118.20 -4.10 1.51e+00 4.39e-01 7.39e+00 angle pdb=" N GLY E 73 " pdb=" CA GLY E 73 " pdb=" C GLY E 73 " ideal model delta sigma weight residual 114.10 118.20 -4.10 1.51e+00 4.39e-01 7.38e+00 angle pdb=" N GLY A 73 " pdb=" CA GLY A 73 " pdb=" C GLY A 73 " ideal model delta sigma weight residual 114.10 118.18 -4.08 1.51e+00 4.39e-01 7.31e+00 ... (remaining 3685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.89: 1476 25.89 - 51.77: 60 51.77 - 77.66: 6 77.66 - 103.54: 0 103.54 - 129.43: 6 Dihedral angle restraints: 1548 sinusoidal: 576 harmonic: 972 Sorted by residual: dihedral pdb=" C33 KDH D 501 " pdb=" C36 KDH D 501 " pdb=" O35 KDH D 501 " pdb=" C38 KDH D 501 " ideal model delta sinusoidal sigma weight residual 166.64 -63.93 -129.43 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C33 KDH A 501 " pdb=" C36 KDH A 501 " pdb=" O35 KDH A 501 " pdb=" C38 KDH A 501 " ideal model delta sinusoidal sigma weight residual 166.64 -64.00 -129.36 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C33 KDH B 501 " pdb=" C36 KDH B 501 " pdb=" O35 KDH B 501 " pdb=" C38 KDH B 501 " ideal model delta sinusoidal sigma weight residual 166.64 -64.02 -129.34 1 3.00e+01 1.11e-03 1.74e+01 ... (remaining 1545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 203 0.037 - 0.074: 139 0.074 - 0.111: 74 0.111 - 0.148: 34 0.148 - 0.185: 12 Chirality restraints: 462 Sorted by residual: chirality pdb=" CB VAL D 40 " pdb=" CA VAL D 40 " pdb=" CG1 VAL D 40 " pdb=" CG2 VAL D 40 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CB VAL F 40 " pdb=" CA VAL F 40 " pdb=" CG1 VAL F 40 " pdb=" CG2 VAL F 40 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CB VAL C 40 " pdb=" CA VAL C 40 " pdb=" CG1 VAL C 40 " pdb=" CG2 VAL C 40 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 459 not shown) Planarity restraints: 438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 50 " 0.012 2.00e-02 2.50e+03 1.05e-02 1.64e+00 pdb=" CG HIS B 50 " -0.022 2.00e-02 2.50e+03 pdb=" ND1 HIS B 50 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS B 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS B 50 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS B 50 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 50 " 0.012 2.00e-02 2.50e+03 1.03e-02 1.60e+00 pdb=" CG HIS A 50 " -0.021 2.00e-02 2.50e+03 pdb=" ND1 HIS A 50 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS A 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS A 50 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS A 50 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 50 " -0.012 2.00e-02 2.50e+03 1.03e-02 1.58e+00 pdb=" CG HIS F 50 " 0.021 2.00e-02 2.50e+03 pdb=" ND1 HIS F 50 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS F 50 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS F 50 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS F 50 " -0.005 2.00e-02 2.50e+03 ... (remaining 435 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 493 2.76 - 3.29: 2485 3.29 - 3.83: 3858 3.83 - 4.36: 4344 4.36 - 4.90: 9687 Nonbonded interactions: 20867 Sorted by model distance: nonbonded pdb=" NE2 GLN C 79 " pdb=" O GLY E 86 " model vdw 2.222 3.120 nonbonded pdb=" O GLY D 86 " pdb=" NE2 GLN B 79 " model vdw 2.228 3.120 nonbonded pdb=" O GLY C 86 " pdb=" NE2 GLN F 79 " model vdw 2.229 3.120 nonbonded pdb=" NE2 GLN D 79 " pdb=" O GLY A 86 " model vdw 2.237 3.120 nonbonded pdb=" C4 KDH C 501 " pdb=" O37 KDH F 501 " model vdw 2.425 3.340 ... (remaining 20862 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'A' selection = chain 'F' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.830 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 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 : 0.010 0.056 2700 Z= 0.432 Angle : 1.016 4.713 3690 Z= 0.530 Chirality : 0.066 0.185 462 Planarity : 0.003 0.010 438 Dihedral : 17.290 129.429 936 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.41 % Favored : 77.59 % Rotamer: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.55 (0.39), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.004 TYR A 39 PHE 0.008 0.003 PHE E 94 HIS 0.008 0.005 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00977 ( 2700) covalent geometry : angle 1.01607 ( 3690) hydrogen bonds : bond 0.18335 ( 20) hydrogen bonds : angle 7.69179 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.067 Fit side-chains REVERT: C 43 LYS cc_start: 0.7848 (ptpp) cc_final: 0.7591 (ptpp) REVERT: E 43 LYS cc_start: 0.8258 (ptpp) cc_final: 0.7936 (ptpp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0740 time to fit residues: 2.5379 Evaluate side-chains 29 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.132757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.089204 restraints weight = 3157.712| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.40 r_work: 0.3190 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2700 Z= 0.162 Angle : 0.713 4.423 3690 Z= 0.380 Chirality : 0.059 0.162 462 Planarity : 0.002 0.008 438 Dihedral : 16.296 90.327 468 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.37 % Favored : 85.63 % Rotamer: Outliers : 3.57 % Allowed : 7.94 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.56 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR F 39 PHE 0.009 0.002 PHE D 94 HIS 0.006 0.003 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 2700) covalent geometry : angle 0.71267 ( 3690) hydrogen bonds : bond 0.02599 ( 20) hydrogen bonds : angle 5.67595 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.095 Fit side-chains REVERT: D 43 LYS cc_start: 0.6825 (ptpp) cc_final: 0.6609 (ptpt) REVERT: E 43 LYS cc_start: 0.7960 (ptpp) cc_final: 0.7720 (ptpp) outliers start: 9 outliers final: 9 residues processed: 32 average time/residue: 0.0876 time to fit residues: 3.3066 Evaluate side-chains 32 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 20 optimal weight: 0.0970 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.128625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.087658 restraints weight = 3424.215| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.35 r_work: 0.3287 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2700 Z= 0.095 Angle : 0.548 3.791 3690 Z= 0.293 Chirality : 0.055 0.136 462 Planarity : 0.001 0.006 438 Dihedral : 14.144 87.501 468 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.51 % Favored : 86.49 % Rotamer: Outliers : 3.57 % Allowed : 7.94 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.72 (0.46), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR F 39 PHE 0.007 0.002 PHE D 94 HIS 0.004 0.002 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 2700) covalent geometry : angle 0.54801 ( 3690) hydrogen bonds : bond 0.01957 ( 20) hydrogen bonds : angle 5.40810 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.065 Fit side-chains REVERT: B 46 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8251 (mt-10) outliers start: 9 outliers final: 9 residues processed: 30 average time/residue: 0.0786 time to fit residues: 2.7836 Evaluate side-chains 30 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.122300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.080966 restraints weight = 3438.881| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.35 r_work: 0.3282 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 2700 Z= 0.209 Angle : 0.631 3.779 3690 Z= 0.345 Chirality : 0.055 0.135 462 Planarity : 0.002 0.009 438 Dihedral : 14.323 84.244 468 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.23 % Favored : 84.77 % Rotamer: Outliers : 6.75 % Allowed : 4.37 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.67 (0.46), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR F 39 PHE 0.010 0.002 PHE D 94 HIS 0.006 0.004 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 2700) covalent geometry : angle 0.63079 ( 3690) hydrogen bonds : bond 0.02320 ( 20) hydrogen bonds : angle 5.47505 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 24 time to evaluate : 0.096 Fit side-chains REVERT: E 43 LYS cc_start: 0.7834 (ptpp) cc_final: 0.7527 (ptpp) outliers start: 17 outliers final: 17 residues processed: 37 average time/residue: 0.0767 time to fit residues: 3.3746 Evaluate side-chains 40 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 23 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.124860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.084634 restraints weight = 3448.172| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.36 r_work: 0.3225 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2700 Z= 0.117 Angle : 0.542 3.971 3690 Z= 0.295 Chirality : 0.053 0.130 462 Planarity : 0.002 0.007 438 Dihedral : 13.447 81.658 468 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.51 % Favored : 86.49 % Rotamer: Outliers : 5.95 % Allowed : 7.54 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.28 (0.47), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 39 PHE 0.008 0.002 PHE D 94 HIS 0.004 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 2700) covalent geometry : angle 0.54191 ( 3690) hydrogen bonds : bond 0.01950 ( 20) hydrogen bonds : angle 5.47776 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 20 time to evaluate : 0.113 Fit side-chains outliers start: 15 outliers final: 14 residues processed: 33 average time/residue: 0.0700 time to fit residues: 2.7943 Evaluate side-chains 32 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 18 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 34 optimal weight: 0.0050 overall best weight: 1.1198 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.125311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.086123 restraints weight = 3526.458| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.40 r_work: 0.3266 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2700 Z= 0.093 Angle : 0.482 3.763 3690 Z= 0.265 Chirality : 0.052 0.128 462 Planarity : 0.001 0.006 438 Dihedral : 12.633 78.665 468 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.93 % Favored : 87.07 % Rotamer: Outliers : 5.95 % Allowed : 7.54 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.48), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR A 39 PHE 0.006 0.001 PHE D 94 HIS 0.004 0.002 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 2700) covalent geometry : angle 0.48241 ( 3690) hydrogen bonds : bond 0.01693 ( 20) hydrogen bonds : angle 5.33931 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 19 time to evaluate : 0.156 Fit side-chains outliers start: 15 outliers final: 15 residues processed: 31 average time/residue: 0.0726 time to fit residues: 2.7179 Evaluate side-chains 34 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 19 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 0.0270 chunk 13 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.9844 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.122122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.081915 restraints weight = 3478.438| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.45 r_work: 0.3187 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2700 Z= 0.139 Angle : 0.526 3.654 3690 Z= 0.292 Chirality : 0.052 0.130 462 Planarity : 0.002 0.008 438 Dihedral : 12.555 76.745 468 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.37 % Favored : 85.63 % Rotamer: Outliers : 5.95 % Allowed : 7.94 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.48), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR F 39 PHE 0.009 0.002 PHE D 94 HIS 0.005 0.003 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 2700) covalent geometry : angle 0.52582 ( 3690) hydrogen bonds : bond 0.01864 ( 20) hydrogen bonds : angle 5.41476 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 20 time to evaluate : 0.094 Fit side-chains outliers start: 15 outliers final: 15 residues processed: 31 average time/residue: 0.0742 time to fit residues: 2.7839 Evaluate side-chains 35 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 20 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 20 optimal weight: 0.0050 chunk 30 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.125245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.086077 restraints weight = 3576.907| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.49 r_work: 0.3449 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2700 Z= 0.092 Angle : 0.475 3.983 3690 Z= 0.263 Chirality : 0.051 0.129 462 Planarity : 0.001 0.006 438 Dihedral : 12.144 75.657 468 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.22 % Favored : 86.78 % Rotamer: Outliers : 5.95 % Allowed : 7.94 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.48), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR A 39 PHE 0.006 0.001 PHE D 94 HIS 0.004 0.002 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 2700) covalent geometry : angle 0.47508 ( 3690) hydrogen bonds : bond 0.01692 ( 20) hydrogen bonds : angle 5.37516 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 18 time to evaluate : 0.093 Fit side-chains REVERT: B 46 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8322 (mt-10) outliers start: 15 outliers final: 15 residues processed: 30 average time/residue: 0.0645 time to fit residues: 2.3369 Evaluate side-chains 33 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 18 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 7.9990 chunk 28 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 27 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 0.0470 chunk 18 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.132282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.088188 restraints weight = 3196.433| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.66 r_work: 0.3277 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2700 Z= 0.104 Angle : 0.476 3.804 3690 Z= 0.266 Chirality : 0.051 0.129 462 Planarity : 0.001 0.007 438 Dihedral : 12.033 74.630 468 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.22 % Favored : 86.78 % Rotamer: Outliers : 5.95 % Allowed : 9.13 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.48), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR D 39 PHE 0.007 0.001 PHE D 94 HIS 0.005 0.002 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 2700) covalent geometry : angle 0.47587 ( 3690) hydrogen bonds : bond 0.01676 ( 20) hydrogen bonds : angle 5.35253 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 19 time to evaluate : 0.092 Fit side-chains outliers start: 15 outliers final: 15 residues processed: 31 average time/residue: 0.0703 time to fit residues: 2.6628 Evaluate side-chains 34 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 19 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 10 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.128401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.083850 restraints weight = 3186.046| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.60 r_work: 0.3166 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2700 Z= 0.225 Angle : 0.599 4.066 3690 Z= 0.334 Chirality : 0.053 0.134 462 Planarity : 0.002 0.009 438 Dihedral : 12.475 74.506 468 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.37 % Favored : 85.63 % Rotamer: Outliers : 5.95 % Allowed : 9.13 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.47), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR A 39 PHE 0.013 0.003 PHE D 94 HIS 0.006 0.004 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 2700) covalent geometry : angle 0.59920 ( 3690) hydrogen bonds : bond 0.02213 ( 20) hydrogen bonds : angle 5.46819 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 21 time to evaluate : 0.092 Fit side-chains outliers start: 15 outliers final: 15 residues processed: 32 average time/residue: 0.0623 time to fit residues: 2.4221 Evaluate side-chains 36 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 21 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.131157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.086841 restraints weight = 3140.014| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.62 r_work: 0.3252 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2700 Z= 0.127 Angle : 0.516 3.942 3690 Z= 0.287 Chirality : 0.052 0.131 462 Planarity : 0.002 0.007 438 Dihedral : 12.151 74.600 468 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.51 % Favored : 86.49 % Rotamer: Outliers : 5.95 % Allowed : 9.52 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.48), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR A 39 PHE 0.008 0.002 PHE D 94 HIS 0.005 0.003 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 2700) covalent geometry : angle 0.51570 ( 3690) hydrogen bonds : bond 0.01858 ( 20) hydrogen bonds : angle 5.44042 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1138.79 seconds wall clock time: 20 minutes 11.12 seconds (1211.12 seconds total)