Starting phenix.real_space_refine on Wed Jul 1 21:23:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zwk_60530/07_2026/8zwk_60530.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zwk_60530/07_2026/8zwk_60530.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/8zwk_60530/07_2026/8zwk_60530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zwk_60530/07_2026/8zwk_60530.map" model { file = "/net/cci-nas-00/data/ceres_data/8zwk_60530/07_2026/8zwk_60530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zwk_60530/07_2026/8zwk_60530.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians P 6 5.49 5 C 1704 2.51 5 N 486 2.21 5 O 564 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2760 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "Q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Restraints were copied for chains: D, E, B, C, F, G Time building chain proxies: 0.65, per 1000 atoms: 0.24 Number of scatterers: 2760 At special positions: 0 Unit cell: (104.58, 97.11, 32.37, 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) P 6 15.00 O 564 8.00 N 486 7.00 C 1704 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: 0.23 Conformation dependent library (CDL) restraints added in 114.6 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 28.6% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 45 through 49 removed outlier: 6.803A pdb=" N GLU D 46 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY A 47 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLU A 46 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N VAL E 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL A 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 52 through 54 removed outlier: 6.518A pdb=" N ALA A 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 61 through 62 removed outlier: 6.541A pdb=" N GLU A 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 65 through 66 removed outlier: 6.884A pdb=" N ASN A 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.613A pdb=" N VAL A 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 74 through 82 removed outlier: 6.933A pdb=" N THR D 75 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA A 76 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N THR A 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N ALA E 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N LYS E 80 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN A 79 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N VAL E 82 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR A 81 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 45 through 49 removed outlier: 6.804A pdb=" N GLU C 46 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY B 47 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLU B 46 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N VAL F 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL B 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 52 through 54 removed outlier: 6.518A pdb=" N ALA B 53 " --> pdb=" O THR F 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 61 through 62 removed outlier: 6.541A pdb=" N GLU B 61 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 65 through 66 removed outlier: 6.885A pdb=" N ASN B 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 69 through 71 removed outlier: 6.613A pdb=" N VAL B 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 74 through 82 removed outlier: 6.932A pdb=" N THR C 75 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA B 76 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N THR B 75 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N ALA F 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL B 77 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N LYS F 80 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN B 79 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N VAL F 82 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR B 81 " --> pdb=" O VAL F 82 " (cutoff:3.500A) 28 hydrogen bonds defined for protein. 84 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 0.34 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.30: 462 1.30 - 1.38: 516 1.38 - 1.46: 365 1.46 - 1.53: 1315 1.53 - 1.61: 130 Bond restraints: 2788 Sorted by residual: bond pdb=" N GLY F 68 " pdb=" CA GLY F 68 " ideal model delta sigma weight residual 1.445 1.450 -0.006 8.30e-03 1.45e+04 4.68e-01 bond pdb=" N GLY E 68 " pdb=" CA GLY E 68 " ideal model delta sigma weight residual 1.445 1.450 -0.005 8.30e-03 1.45e+04 3.84e-01 bond pdb=" N GLY B 68 " pdb=" CA GLY B 68 " ideal model delta sigma weight residual 1.445 1.450 -0.005 8.30e-03 1.45e+04 3.63e-01 bond pdb=" N GLY C 68 " pdb=" CA GLY C 68 " ideal model delta sigma weight residual 1.445 1.449 -0.005 8.30e-03 1.45e+04 3.47e-01 bond pdb=" N GLY D 68 " pdb=" CA GLY D 68 " ideal model delta sigma weight residual 1.445 1.449 -0.005 8.30e-03 1.45e+04 3.27e-01 ... (remaining 2783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.79: 3303 0.79 - 1.58: 355 1.58 - 2.37: 101 2.37 - 3.16: 25 3.16 - 3.95: 12 Bond angle restraints: 3796 Sorted by residual: angle pdb=" N SER D 42 " pdb=" CA SER D 42 " pdb=" C SER D 42 " ideal model delta sigma weight residual 110.80 114.75 -3.95 2.13e+00 2.20e-01 3.44e+00 angle pdb=" N SER C 42 " pdb=" CA SER C 42 " pdb=" C SER C 42 " ideal model delta sigma weight residual 110.80 114.74 -3.94 2.13e+00 2.20e-01 3.42e+00 angle pdb=" N SER B 42 " pdb=" CA SER B 42 " pdb=" C SER B 42 " ideal model delta sigma weight residual 110.80 114.74 -3.94 2.13e+00 2.20e-01 3.42e+00 angle pdb=" N SER A 42 " pdb=" CA SER A 42 " pdb=" C SER A 42 " ideal model delta sigma weight residual 110.80 114.74 -3.94 2.13e+00 2.20e-01 3.41e+00 angle pdb=" N SER E 42 " pdb=" CA SER E 42 " pdb=" C SER E 42 " ideal model delta sigma weight residual 110.80 114.72 -3.92 2.13e+00 2.20e-01 3.39e+00 ... (remaining 3791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.43: 1550 24.43 - 48.86: 46 48.86 - 73.29: 12 73.29 - 97.71: 0 97.71 - 122.14: 6 Dihedral angle restraints: 1614 sinusoidal: 588 harmonic: 1026 Sorted by residual: dihedral pdb=" CA GLY A 41 " pdb=" C GLY A 41 " pdb=" N SER A 42 " pdb=" CA SER A 42 " ideal model delta harmonic sigma weight residual -180.00 -158.33 -21.67 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLY F 41 " pdb=" C GLY F 41 " pdb=" N SER F 42 " pdb=" CA SER F 42 " ideal model delta harmonic sigma weight residual -180.00 -158.33 -21.67 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLY E 41 " pdb=" C GLY E 41 " pdb=" N SER E 42 " pdb=" CA SER E 42 " ideal model delta harmonic sigma weight residual -180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 1611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 263 0.027 - 0.054: 112 0.054 - 0.081: 51 0.081 - 0.108: 37 0.108 - 0.135: 35 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA VAL C 49 " pdb=" N VAL C 49 " pdb=" C VAL C 49 " pdb=" CB VAL C 49 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA VAL D 49 " pdb=" N VAL D 49 " pdb=" C VAL D 49 " pdb=" CB VAL D 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 495 not shown) Planarity restraints: 450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS F 43 " -0.003 2.00e-02 2.50e+03 6.65e-03 4.42e-01 pdb=" C LYS F 43 " 0.012 2.00e-02 2.50e+03 pdb=" O LYS F 43 " -0.004 2.00e-02 2.50e+03 pdb=" N THR F 44 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 43 " -0.003 2.00e-02 2.50e+03 6.62e-03 4.38e-01 pdb=" C LYS B 43 " 0.011 2.00e-02 2.50e+03 pdb=" O LYS B 43 " -0.004 2.00e-02 2.50e+03 pdb=" N THR B 44 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 43 " 0.003 2.00e-02 2.50e+03 6.61e-03 4.37e-01 pdb=" C LYS A 43 " -0.011 2.00e-02 2.50e+03 pdb=" O LYS A 43 " 0.004 2.00e-02 2.50e+03 pdb=" N THR A 44 " 0.004 2.00e-02 2.50e+03 ... (remaining 447 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 527 2.78 - 3.31: 2457 3.31 - 3.84: 4297 3.84 - 4.37: 4504 4.37 - 4.90: 9330 Nonbonded interactions: 21115 Sorted by model distance: nonbonded pdb=" OE2 GLU C 46 " pdb=" NZ LYS C 80 " model vdw 2.253 3.120 nonbonded pdb=" OE2 GLU F 46 " pdb=" NZ LYS F 80 " model vdw 2.253 3.120 nonbonded pdb=" OE2 GLU D 46 " pdb=" NZ LYS D 80 " model vdw 2.253 3.120 nonbonded pdb=" OE2 GLU E 46 " pdb=" NZ LYS E 80 " model vdw 2.254 3.120 nonbonded pdb=" OE2 GLU A 46 " pdb=" NZ LYS A 80 " model vdw 2.254 3.120 ... (remaining 21110 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' selection = chain 'B' selection = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'Q' selection = chain 'G' } 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: 3.420 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.700 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 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 : 0.003 0.016 2788 Z= 0.158 Angle : 0.602 3.950 3796 Z= 0.345 Chirality : 0.052 0.135 498 Planarity : 0.002 0.007 450 Dihedral : 16.324 122.139 966 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.39 (0.27), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.10 (0.21), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR F 39 PHE 0.003 0.001 PHE F 94 HIS 0.003 0.002 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 ( 2788) covalent geometry : angle 0.60201 / 0.35 ( 3796) hydrogen bonds : bond 0.21901 / 11.99 ( 28) hydrogen bonds : angle 8.52070 / 5.26 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.095 Fit side-chains REVERT: A 83 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7257 (tp30) REVERT: D 83 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7523 (tp30) REVERT: E 83 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7494 (tp30) REVERT: B 37 VAL cc_start: 0.6552 (m) cc_final: 0.6225 (m) REVERT: B 43 LYS cc_start: 0.6199 (ptpt) cc_final: 0.5442 (tttp) REVERT: B 83 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7353 (tp30) REVERT: F 83 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7593 (tp30) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0736 time to fit residues: 3.1521 Evaluate side-chains 26 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.058 ------------------------------------------------------------------------------- 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: 7.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.172495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.132301 restraints weight = 2871.825| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.44 r_work: 0.3861 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 2788 Z= 0.264 Angle : 0.725 5.331 3796 Z= 0.405 Chirality : 0.054 0.134 498 Planarity : 0.003 0.010 450 Dihedral : 15.975 115.573 444 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 8.52 % Allowed : 3.70 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.87 (0.29), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.22), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.004 TYR E 39 PHE 0.013 0.003 PHE A 94 HIS 0.006 0.003 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.26 ( 2788) covalent geometry : angle 0.72496 / 0.40 ( 3796) hydrogen bonds : bond 0.03726 / 2.02 ( 28) hydrogen bonds : angle 7.44876 / 4.75 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 25 time to evaluate : 0.106 Fit side-chains REVERT: A 60 LYS cc_start: 0.6833 (mttt) cc_final: 0.6388 (mtpt) REVERT: A 83 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7617 (tp30) REVERT: D 60 LYS cc_start: 0.6712 (mttt) cc_final: 0.6360 (mtpt) REVERT: D 83 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7831 (tp30) REVERT: E 60 LYS cc_start: 0.7351 (mttt) cc_final: 0.6909 (mtpt) REVERT: E 83 GLU cc_start: 0.8483 (mt-10) cc_final: 0.7743 (tp30) REVERT: B 60 LYS cc_start: 0.6805 (mttt) cc_final: 0.6426 (mtpt) REVERT: C 60 LYS cc_start: 0.6666 (mttt) cc_final: 0.6206 (mtpt) REVERT: C 83 GLU cc_start: 0.8522 (mt-10) cc_final: 0.7878 (tp30) REVERT: F 60 LYS cc_start: 0.7350 (mttt) cc_final: 0.6976 (mtpt) REVERT: F 83 GLU cc_start: 0.8589 (mt-10) cc_final: 0.7996 (tp30) outliers start: 23 outliers final: 23 residues processed: 47 average time/residue: 0.0867 time to fit residues: 4.6883 Evaluate side-chains 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 25 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 33 optimal weight: 0.0070 chunk 26 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.175082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.132589 restraints weight = 2809.261| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.45 r_work: 0.3879 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2788 Z= 0.236 Angle : 0.676 4.562 3796 Z= 0.372 Chirality : 0.053 0.131 498 Planarity : 0.003 0.009 450 Dihedral : 14.825 107.862 444 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 6.67 % Allowed : 7.78 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.57 (0.29), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.22), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR D 39 PHE 0.013 0.003 PHE A 94 HIS 0.007 0.004 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.24 ( 2788) covalent geometry : angle 0.67610 / 0.37 ( 3796) hydrogen bonds : bond 0.04877 / 2.73 ( 28) hydrogen bonds : angle 7.38658 / 4.75 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 32 time to evaluate : 0.059 Fit side-chains REVERT: A 60 LYS cc_start: 0.6967 (mttt) cc_final: 0.6547 (mtpt) REVERT: D 60 LYS cc_start: 0.6802 (mttt) cc_final: 0.6384 (mtpt) REVERT: D 83 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7939 (tp30) REVERT: E 60 LYS cc_start: 0.7388 (mttt) cc_final: 0.6933 (mtpt) REVERT: E 83 GLU cc_start: 0.8509 (mt-10) cc_final: 0.7920 (tp30) REVERT: B 37 VAL cc_start: 0.7155 (OUTLIER) cc_final: 0.6786 (m) REVERT: B 60 LYS cc_start: 0.6789 (mttt) cc_final: 0.6434 (mtpt) REVERT: C 60 LYS cc_start: 0.6812 (mttt) cc_final: 0.6443 (mtpt) REVERT: F 60 LYS cc_start: 0.7432 (mttt) cc_final: 0.6964 (mtpt) REVERT: F 83 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8063 (tp30) outliers start: 18 outliers final: 17 residues processed: 44 average time/residue: 0.0588 time to fit residues: 2.9888 Evaluate side-chains 50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 32 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.178511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.135581 restraints weight = 2707.809| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.42 r_work: 0.3730 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2788 Z= 0.154 Angle : 0.598 4.871 3796 Z= 0.327 Chirality : 0.051 0.127 498 Planarity : 0.002 0.008 450 Dihedral : 14.403 104.759 444 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 7.78 % Allowed : 7.78 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.20 (0.32), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.24), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR F 39 PHE 0.012 0.003 PHE A 94 HIS 0.006 0.003 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 2788) covalent geometry : angle 0.59760 / 0.33 ( 3796) hydrogen bonds : bond 0.02689 / 1.46 ( 28) hydrogen bonds : angle 7.19801 / 4.63 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 28 time to evaluate : 0.054 Fit side-chains REVERT: A 37 VAL cc_start: 0.6683 (OUTLIER) cc_final: 0.6289 (m) REVERT: A 60 LYS cc_start: 0.6537 (mttt) cc_final: 0.6149 (mtpt) REVERT: D 60 LYS cc_start: 0.6535 (mttt) cc_final: 0.6138 (mtpt) REVERT: D 83 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7865 (tp30) REVERT: E 60 LYS cc_start: 0.7206 (mttt) cc_final: 0.6728 (mtpt) REVERT: E 83 GLU cc_start: 0.8560 (mt-10) cc_final: 0.7858 (tp30) REVERT: B 37 VAL cc_start: 0.6876 (OUTLIER) cc_final: 0.6535 (m) REVERT: B 60 LYS cc_start: 0.6431 (mttt) cc_final: 0.6097 (mtpt) REVERT: C 60 LYS cc_start: 0.6555 (mttt) cc_final: 0.6153 (mtpt) REVERT: F 60 LYS cc_start: 0.7249 (mttt) cc_final: 0.6775 (mtpt) REVERT: F 83 GLU cc_start: 0.8651 (mt-10) cc_final: 0.7992 (tp30) outliers start: 21 outliers final: 18 residues processed: 43 average time/residue: 0.0592 time to fit residues: 2.9745 Evaluate side-chains 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 28 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 0.3980 chunk 17 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.0870 overall best weight: 2.2964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.178897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.135438 restraints weight = 2636.184| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.38 r_work: 0.3751 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3640 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2788 Z= 0.163 Angle : 0.585 4.415 3796 Z= 0.320 Chirality : 0.050 0.128 498 Planarity : 0.002 0.008 450 Dihedral : 13.960 102.358 444 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 7.41 % Allowed : 9.63 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR B 39 PHE 0.011 0.003 PHE A 94 HIS 0.006 0.003 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 2788) covalent geometry : angle 0.58523 / 0.32 ( 3796) hydrogen bonds : bond 0.02784 / 1.53 ( 28) hydrogen bonds : angle 7.13391 / 4.60 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 28 time to evaluate : 0.129 Fit side-chains REVERT: A 37 VAL cc_start: 0.6739 (OUTLIER) cc_final: 0.6332 (m) REVERT: A 60 LYS cc_start: 0.6584 (mttt) cc_final: 0.6229 (mtpt) REVERT: D 60 LYS cc_start: 0.6615 (mttt) cc_final: 0.6211 (mtpt) REVERT: D 83 GLU cc_start: 0.8485 (mt-10) cc_final: 0.7843 (tp30) REVERT: E 60 LYS cc_start: 0.7152 (mttt) cc_final: 0.6714 (mtpt) REVERT: E 83 GLU cc_start: 0.8609 (mt-10) cc_final: 0.7936 (tp30) REVERT: B 37 VAL cc_start: 0.6956 (OUTLIER) cc_final: 0.6607 (m) REVERT: B 60 LYS cc_start: 0.6482 (mttt) cc_final: 0.6160 (mtpt) REVERT: C 60 LYS cc_start: 0.6618 (mttt) cc_final: 0.6238 (mtpt) REVERT: F 60 LYS cc_start: 0.7249 (mttt) cc_final: 0.6780 (mtpt) REVERT: F 83 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8007 (tp30) outliers start: 20 outliers final: 18 residues processed: 44 average time/residue: 0.0718 time to fit residues: 3.6902 Evaluate side-chains 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 28 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.181928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.138090 restraints weight = 2663.989| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.39 r_work: 0.3759 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2788 Z= 0.151 Angle : 0.570 4.485 3796 Z= 0.312 Chirality : 0.050 0.126 498 Planarity : 0.002 0.007 450 Dihedral : 13.575 99.883 444 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 8.52 % Allowed : 10.37 % Favored : 81.11 % 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 are not related in a simple way. whole: -3.75 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.003 TYR C 39 PHE 0.012 0.003 PHE B 94 HIS 0.006 0.003 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 2788) covalent geometry : angle 0.57010 / 0.31 ( 3796) hydrogen bonds : bond 0.02550 / 1.41 ( 28) hydrogen bonds : angle 7.05976 / 4.54 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 26 time to evaluate : 0.118 Fit side-chains REVERT: A 37 VAL cc_start: 0.6762 (OUTLIER) cc_final: 0.6352 (m) REVERT: A 60 LYS cc_start: 0.6640 (mttt) cc_final: 0.6283 (mtpt) REVERT: D 60 LYS cc_start: 0.6635 (mttt) cc_final: 0.6238 (mtpt) REVERT: D 83 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7834 (tp30) REVERT: E 60 LYS cc_start: 0.7168 (mttt) cc_final: 0.6747 (mtpt) REVERT: E 83 GLU cc_start: 0.8618 (mt-10) cc_final: 0.7960 (tp30) REVERT: B 37 VAL cc_start: 0.6943 (OUTLIER) cc_final: 0.6594 (m) REVERT: B 60 LYS cc_start: 0.6596 (mttt) cc_final: 0.6217 (mtpt) REVERT: C 60 LYS cc_start: 0.6685 (mttt) cc_final: 0.6306 (mtpt) REVERT: F 60 LYS cc_start: 0.7258 (mttt) cc_final: 0.6769 (mtpt) REVERT: F 83 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8043 (tp30) outliers start: 23 outliers final: 21 residues processed: 45 average time/residue: 0.0881 time to fit residues: 4.6141 Evaluate side-chains 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 26 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.180220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.135830 restraints weight = 2615.771| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.40 r_work: 0.3914 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3805 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2788 Z= 0.185 Angle : 0.600 4.544 3796 Z= 0.329 Chirality : 0.050 0.130 498 Planarity : 0.002 0.008 450 Dihedral : 13.414 98.256 444 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 8.52 % Allowed : 10.37 % Favored : 81.11 % 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 are not related in a simple way. whole: -3.87 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR B 39 PHE 0.013 0.003 PHE A 94 HIS 0.007 0.004 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 ( 2788) covalent geometry : angle 0.59959 / 0.33 ( 3796) hydrogen bonds : bond 0.02745 / 1.51 ( 28) hydrogen bonds : angle 7.17912 / 4.61 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 30 time to evaluate : 0.094 Fit side-chains REVERT: A 37 VAL cc_start: 0.6925 (OUTLIER) cc_final: 0.6509 (m) REVERT: A 60 LYS cc_start: 0.6967 (mttt) cc_final: 0.6590 (mtpt) REVERT: D 60 LYS cc_start: 0.6879 (mttt) cc_final: 0.6468 (mtpt) REVERT: E 60 LYS cc_start: 0.7253 (mttt) cc_final: 0.6855 (mtpt) REVERT: E 83 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8030 (tp30) REVERT: B 37 VAL cc_start: 0.7125 (OUTLIER) cc_final: 0.6755 (m) REVERT: B 60 LYS cc_start: 0.6904 (mttt) cc_final: 0.6537 (mtpt) REVERT: C 60 LYS cc_start: 0.6967 (mttt) cc_final: 0.6560 (mtpt) REVERT: F 60 LYS cc_start: 0.7445 (mttt) cc_final: 0.6973 (mtpt) REVERT: F 83 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8042 (tp30) outliers start: 23 outliers final: 21 residues processed: 46 average time/residue: 0.0809 time to fit residues: 4.3655 Evaluate side-chains 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 30 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 26 optimal weight: 0.0970 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 3 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.186656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.141864 restraints weight = 2615.857| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 2.42 r_work: 0.4000 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3889 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 2788 Z= 0.082 Angle : 0.504 4.436 3796 Z= 0.276 Chirality : 0.050 0.134 498 Planarity : 0.002 0.007 450 Dihedral : 13.136 98.172 444 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 6.30 % Allowed : 12.22 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.37), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR B 39 PHE 0.009 0.002 PHE A 94 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00147 / 0.08 ( 2788) covalent geometry : angle 0.50419 / 0.28 ( 3796) hydrogen bonds : bond 0.02066 / 1.14 ( 28) hydrogen bonds : angle 6.85031 / 4.41 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 25 time to evaluate : 0.106 Fit side-chains REVERT: A 37 VAL cc_start: 0.6925 (OUTLIER) cc_final: 0.6516 (m) REVERT: A 60 LYS cc_start: 0.6928 (mttt) cc_final: 0.6550 (mtpt) REVERT: D 60 LYS cc_start: 0.6850 (mttt) cc_final: 0.6442 (mtpt) REVERT: E 60 LYS cc_start: 0.7346 (mttt) cc_final: 0.6941 (mtpt) REVERT: E 83 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8039 (tp30) REVERT: B 60 LYS cc_start: 0.6899 (mttt) cc_final: 0.6519 (mtpt) REVERT: C 60 LYS cc_start: 0.6925 (mttt) cc_final: 0.6502 (mtpt) REVERT: F 60 LYS cc_start: 0.7368 (mttt) cc_final: 0.6897 (mtpt) REVERT: F 83 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8065 (tp30) outliers start: 17 outliers final: 13 residues processed: 38 average time/residue: 0.1046 time to fit residues: 4.5447 Evaluate side-chains 39 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 25 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 0.0010 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.182332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.137855 restraints weight = 2694.029| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.39 r_work: 0.3916 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3808 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2788 Z= 0.186 Angle : 0.588 4.375 3796 Z= 0.323 Chirality : 0.050 0.129 498 Planarity : 0.002 0.008 450 Dihedral : 13.117 95.973 444 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 5.93 % Allowed : 13.33 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR E 39 PHE 0.012 0.003 PHE B 94 HIS 0.006 0.004 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 ( 2788) covalent geometry : angle 0.58801 / 0.32 ( 3796) hydrogen bonds : bond 0.02451 / 1.35 ( 28) hydrogen bonds : angle 7.07399 / 4.56 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 29 time to evaluate : 0.111 Fit side-chains REVERT: A 37 VAL cc_start: 0.6881 (OUTLIER) cc_final: 0.6466 (m) REVERT: A 60 LYS cc_start: 0.6913 (mttt) cc_final: 0.6548 (mtpt) REVERT: D 60 LYS cc_start: 0.6821 (mttt) cc_final: 0.6429 (mtpt) REVERT: E 60 LYS cc_start: 0.7356 (mttt) cc_final: 0.6961 (mtpt) REVERT: E 83 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8013 (tp30) REVERT: B 60 LYS cc_start: 0.6847 (mttt) cc_final: 0.6492 (mtpt) REVERT: C 60 LYS cc_start: 0.6936 (mttt) cc_final: 0.6527 (mtpt) REVERT: F 60 LYS cc_start: 0.7431 (mttt) cc_final: 0.6960 (mtpt) REVERT: F 83 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8050 (tp30) outliers start: 16 outliers final: 15 residues processed: 38 average time/residue: 0.0935 time to fit residues: 4.1054 Evaluate side-chains 45 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 29 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.176682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.131694 restraints weight = 2747.373| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.45 r_work: 0.3852 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2788 Z= 0.249 Angle : 0.677 4.897 3796 Z= 0.372 Chirality : 0.051 0.134 498 Planarity : 0.003 0.010 450 Dihedral : 13.130 94.100 444 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 7.41 % Allowed : 12.22 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.98 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.004 TYR B 39 PHE 0.018 0.005 PHE B 94 HIS 0.009 0.005 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.25 ( 2788) covalent geometry : angle 0.67652 / 0.37 ( 3796) hydrogen bonds : bond 0.02926 / 1.59 ( 28) hydrogen bonds : angle 7.37026 / 4.75 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 30 time to evaluate : 0.097 Fit side-chains REVERT: A 37 VAL cc_start: 0.6948 (OUTLIER) cc_final: 0.6541 (m) REVERT: A 60 LYS cc_start: 0.6947 (mttt) cc_final: 0.6589 (mtpt) REVERT: D 60 LYS cc_start: 0.6926 (mttt) cc_final: 0.6557 (mtpt) REVERT: E 60 LYS cc_start: 0.7371 (mttt) cc_final: 0.6990 (mtpt) REVERT: E 83 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8065 (tp30) REVERT: B 37 VAL cc_start: 0.7151 (OUTLIER) cc_final: 0.6723 (m) REVERT: B 60 LYS cc_start: 0.6965 (mttt) cc_final: 0.6626 (mtpt) REVERT: C 37 VAL cc_start: 0.7431 (OUTLIER) cc_final: 0.7111 (m) REVERT: C 60 LYS cc_start: 0.7047 (mttt) cc_final: 0.6644 (mtpt) REVERT: F 60 LYS cc_start: 0.7526 (mttt) cc_final: 0.7056 (mtpt) REVERT: F 83 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8047 (tp30) outliers start: 20 outliers final: 15 residues processed: 43 average time/residue: 0.0709 time to fit residues: 3.5410 Evaluate side-chains 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 30 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 0.0980 chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 0.0570 chunk 10 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 0.0050 overall best weight: 0.2450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.188815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.143576 restraints weight = 2511.787| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.39 r_work: 0.3824 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2788 Z= 0.085 Angle : 0.515 4.235 3796 Z= 0.279 Chirality : 0.050 0.130 498 Planarity : 0.002 0.008 450 Dihedral : 12.759 95.157 444 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 5.56 % Allowed : 13.70 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.64 (0.36), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR C 39 PHE 0.010 0.002 PHE A 94 HIS 0.003 0.002 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00163 / 0.08 ( 2788) covalent geometry : angle 0.51462 / 0.28 ( 3796) hydrogen bonds : bond 0.02113 / 1.13 ( 28) hydrogen bonds : angle 6.71634 / 4.35 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 929.39 seconds wall clock time: 16 minutes 45.98 seconds (1005.98 seconds total)