Starting phenix.real_space_refine on Tue Aug 4 12:28:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zwk_60530/08_2026/8zwk_60530.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zwk_60530/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zwk_60530/08_2026/8zwk_60530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zwk_60530/08_2026/8zwk_60530.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zwk_60530/08_2026/8zwk_60530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zwk_60530/08_2026/8zwk_60530.map" } 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-2.2rc3-6140/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: 0.22 Conformation dependent library (CDL) restraints added in 115.6 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: 0.36 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: 0.37 Time building geometry restraints manager: 0.29 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=" C4' A G 12 " pdb=" C3' A G 12 " ideal model delta sigma weight residual 1.521 1.514 0.007 1.00e-02 1.00e+04 4.46e-01 bond pdb=" C4' A Q 12 " pdb=" C3' A Q 12 " ideal model delta sigma weight residual 1.521 1.514 0.007 1.00e-02 1.00e+04 4.31e-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=" C4' A Q 14 " pdb=" C3' A Q 14 " ideal model delta sigma weight residual 1.521 1.515 0.006 1.00e-02 1.00e+04 3.80e-01 ... (remaining 2783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.79: 3285 0.79 - 1.58: 355 1.58 - 2.37: 111 2.37 - 3.16: 33 3.16 - 3.95: 12 Bond angle restraints: 3796 Sorted by residual: angle pdb=" O5' A Q 14 " pdb=" C5' A Q 14 " pdb=" C4' A Q 14 " ideal model delta sigma weight residual 109.40 111.79 -2.39 8.00e-01 1.56e+00 8.95e+00 angle pdb=" O5' A G 14 " pdb=" C5' A G 14 " pdb=" C4' A G 14 " ideal model delta sigma weight residual 109.40 111.79 -2.39 8.00e-01 1.56e+00 8.92e+00 angle pdb=" O5' A Q 12 " pdb=" C5' A Q 12 " pdb=" C4' A Q 12 " ideal model delta sigma weight residual 109.40 111.76 -2.36 8.00e-01 1.56e+00 8.72e+00 angle pdb=" O5' A G 12 " pdb=" C5' A G 12 " pdb=" C4' A G 12 " ideal model delta sigma weight residual 109.40 111.72 -2.32 8.00e-01 1.56e+00 8.39e+00 angle pdb=" O5' A G 13 " pdb=" C5' A G 13 " pdb=" C4' A G 13 " ideal model delta sigma weight residual 109.40 111.69 -2.29 8.00e-01 1.56e+00 8.21e+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 - 0.030: 275 0.030 - 0.059: 109 0.059 - 0.089: 40 0.089 - 0.118: 43 0.118 - 0.148: 31 Chirality restraints: 498 Sorted by residual: chirality pdb=" C2' A G 13 " pdb=" C3' A G 13 " pdb=" O2' A G 13 " pdb=" C1' A G 13 " both_signs ideal model delta sigma weight residual False -2.62 -2.77 0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" C2' A G 12 " pdb=" C3' A G 12 " pdb=" O2' A G 12 " pdb=" C1' A G 12 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" C2' A Q 14 " pdb=" C3' A Q 14 " pdb=" O2' A Q 14 " pdb=" C1' A Q 14 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 5.15e-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: 3.620 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.950 Find NCS groups from input model: 0.040 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.090 ------------------------------------------------------------------------------- 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= 0.162 Angle : 0.625 3.950 3796 Z= 0.370 Chirality : 0.054 0.148 498 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 0.00322 / 0.16 ( 2788) covalent geometry : angle 0.62480 / 0.37 ( 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 : 0.058 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: 0.0496 time to fit residues: 2.1339 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 : 0.056 ------------------------------------------------------------------------------- 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 = 0.4416 r_free = 0.4416 target = 0.172744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.132471 restraints weight = 2868.528| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 2.44 r_work: 0.3861 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 2788 Z= 0.266 Angle : 0.741 5.475 3796 Z= 0.413 Chirality : 0.054 0.130 498 Planarity : 0.003 0.010 450 Dihedral : 15.830 112.620 444 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 8.52 % Allowed : 3.33 % Favored : 88.15 % 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 : -3.70 (0.22), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.004 TYR E 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 0.00572 / 0.27 ( 2788) covalent geometry : angle 0.74091 / 0.41 ( 3796) hydrogen bonds : bond 0.03395 / 1.85 ( 28) hydrogen bonds : angle 7.50829 / 4.79 ( 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 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 26 time to evaluate : 0.085 Fit side-chains REVERT: A 60 LYS cc_start: 0.6861 (mttt) cc_final: 0.6413 (mtpt) REVERT: A 83 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7633 (tp30) REVERT: D 60 LYS cc_start: 0.6716 (mttt) cc_final: 0.6366 (mtpt) REVERT: D 83 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7826 (tp30) REVERT: E 60 LYS cc_start: 0.7356 (mttt) cc_final: 0.6923 (mtpt) REVERT: E 83 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7748 (tp30) REVERT: B 60 LYS cc_start: 0.6796 (mttt) cc_final: 0.6425 (mtpt) REVERT: C 60 LYS cc_start: 0.6682 (mttt) cc_final: 0.6270 (mtpt) REVERT: C 83 GLU cc_start: 0.8529 (mt-10) cc_final: 0.7899 (tp30) REVERT: F 60 LYS cc_start: 0.7301 (mttt) cc_final: 0.6946 (mtpt) REVERT: F 83 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8013 (tp30) outliers start: 23 outliers final: 23 residues processed: 48 average time/residue: 0.0807 time to fit residues: 4.4775 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 : 0.058 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 11 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 26 optimal weight: 0.0670 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.9724 ------------------------------------------------------------------------------- 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 = 0.4448 r_free = 0.4448 target = 0.175926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.133915 restraints weight = 2797.525| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 2.43 r_work: 0.3901 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1723 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= 0.194 Angle : 0.628 4.510 3796 Z= 0.344 Chirality : 0.051 0.126 498 Planarity : 0.002 0.008 450 Dihedral : 14.943 107.492 444 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 6.67 % Allowed : 6.30 % Favored : 87.04 % 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: -4.50 (0.30), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.23), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR E 39 PHE 0.012 0.003 PHE A 94 HIS 0.007 0.004 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 ( 2788) covalent geometry : angle 0.62809 / 0.34 ( 3796) hydrogen bonds : bond 0.04239 / 2.34 ( 28) hydrogen bonds : angle 7.25515 / 4.67 ( 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 44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 26 time to evaluate : 0.058 Fit side-chains REVERT: A 60 LYS cc_start: 0.6910 (mttt) cc_final: 0.6479 (mtpt) REVERT: D 60 LYS cc_start: 0.6703 (mttt) cc_final: 0.6372 (mtpt) REVERT: D 83 GLU cc_start: 0.8449 (mt-10) cc_final: 0.7908 (tp30) REVERT: E 60 LYS cc_start: 0.7383 (mttt) cc_final: 0.6915 (mtpt) REVERT: B 37 VAL cc_start: 0.7104 (OUTLIER) cc_final: 0.6679 (m) REVERT: B 60 LYS cc_start: 0.6767 (mttt) cc_final: 0.6405 (mtpt) REVERT: C 37 VAL cc_start: 0.7351 (OUTLIER) cc_final: 0.7059 (m) REVERT: C 60 LYS cc_start: 0.6733 (mttt) cc_final: 0.6290 (mtpt) REVERT: F 60 LYS cc_start: 0.7432 (mttt) cc_final: 0.6969 (mtpt) REVERT: F 83 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8033 (tp30) outliers start: 18 outliers final: 15 residues processed: 41 average time/residue: 0.0984 time to fit residues: 4.6018 Evaluate side-chains 43 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 26 time to evaluate : 0.096 ------------------------------------------------------------------------------- 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 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 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 79 GLN 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: 6.9990 chunk 5 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 0.0000 chunk 16 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 overall best weight: 1.2988 ------------------------------------------------------------------------------- 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 = 0.4515 r_free = 0.4515 target = 0.183515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.140860 restraints weight = 2662.957| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.38 r_work: 0.3790 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2788 Z= 0.104 Angle : 0.535 4.671 3796 Z= 0.292 Chirality : 0.050 0.133 498 Planarity : 0.002 0.007 450 Dihedral : 14.354 103.681 444 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 6.30 % Allowed : 8.52 % Favored : 85.19 % 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: -4.03 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR F 39 PHE 0.010 0.002 PHE A 94 HIS 0.005 0.002 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 2788) covalent geometry : angle 0.53548 / 0.29 ( 3796) hydrogen bonds : bond 0.02161 / 1.16 ( 28) hydrogen bonds : angle 6.96996 / 4.49 ( 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 37 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 20 time to evaluate : 0.098 Fit side-chains REVERT: A 37 VAL cc_start: 0.6687 (OUTLIER) cc_final: 0.6277 (m) REVERT: D 83 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7922 (tp30) REVERT: E 60 LYS cc_start: 0.7236 (mttt) cc_final: 0.6783 (mtpt) REVERT: E 83 GLU cc_start: 0.8556 (mt-10) cc_final: 0.7870 (tp30) REVERT: B 60 LYS cc_start: 0.6471 (mttt) cc_final: 0.6149 (mtpt) REVERT: F 60 LYS cc_start: 0.7268 (mttt) cc_final: 0.6785 (mtpt) REVERT: F 83 GLU cc_start: 0.8632 (mt-10) cc_final: 0.7995 (tp30) outliers start: 17 outliers final: 15 residues processed: 34 average time/residue: 0.0871 time to fit residues: 3.4922 Evaluate side-chains 36 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 20 time to evaluate : 0.095 ------------------------------------------------------------------------------- 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 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 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 C residue 75 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.4419 r_free = 0.4419 target = 0.173365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.130357 restraints weight = 2708.931| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.42 r_work: 0.3845 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 2788 Z= 0.270 Angle : 0.708 4.762 3796 Z= 0.392 Chirality : 0.053 0.132 498 Planarity : 0.003 0.010 450 Dihedral : 14.101 100.020 444 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 8.52 % Allowed : 7.78 % Favored : 83.70 % 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: -4.11 (0.32), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.005 TYR B 39 PHE 0.014 0.004 PHE A 94 HIS 0.009 0.005 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.27 ( 2788) covalent geometry : angle 0.70755 / 0.39 ( 3796) hydrogen bonds : bond 0.03026 / 1.68 ( 28) hydrogen bonds : angle 7.47142 / 4.79 ( 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 52 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 29 time to evaluate : 0.059 Fit side-chains REVERT: A 37 VAL cc_start: 0.7037 (OUTLIER) cc_final: 0.6641 (m) REVERT: A 60 LYS cc_start: 0.6999 (mttt) cc_final: 0.6601 (mtpt) REVERT: D 60 LYS cc_start: 0.6902 (mttt) cc_final: 0.6494 (mtpt) REVERT: D 83 GLU cc_start: 0.8485 (mt-10) cc_final: 0.7943 (tp30) REVERT: E 60 LYS cc_start: 0.7349 (mttt) cc_final: 0.6930 (mtpt) REVERT: E 83 GLU cc_start: 0.8535 (mt-10) cc_final: 0.7984 (tp30) REVERT: B 37 VAL cc_start: 0.7203 (OUTLIER) cc_final: 0.6822 (m) REVERT: B 60 LYS cc_start: 0.6871 (mttt) cc_final: 0.6527 (mtpt) REVERT: C 60 LYS cc_start: 0.6883 (mttt) cc_final: 0.6499 (mtpt) REVERT: F 60 LYS cc_start: 0.7422 (mttt) cc_final: 0.6954 (mtpt) REVERT: F 83 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8049 (tp30) outliers start: 23 outliers final: 20 residues processed: 46 average time/residue: 0.0545 time to fit residues: 2.9304 Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 29 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.0370 chunk 12 optimal weight: 0.0470 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.1760 ------------------------------------------------------------------------------- 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 = 0.4509 r_free = 0.4509 target = 0.182991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.139416 restraints weight = 2623.282| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.38 r_work: 0.3778 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2788 Z= 0.105 Angle : 0.540 4.505 3796 Z= 0.293 Chirality : 0.050 0.128 498 Planarity : 0.002 0.008 450 Dihedral : 13.690 99.753 444 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 7.41 % Allowed : 8.89 % Favored : 83.70 % 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: -3.82 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR F 39 PHE 0.012 0.003 PHE B 94 HIS 0.005 0.002 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 2788) covalent geometry : angle 0.54027 / 0.29 ( 3796) hydrogen bonds : bond 0.02371 / 1.29 ( 28) hydrogen bonds : angle 7.06822 / 4.55 ( 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 46 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 26 time to evaluate : 0.098 Fit side-chains REVERT: A 37 VAL cc_start: 0.6699 (OUTLIER) cc_final: 0.6263 (m) REVERT: A 60 LYS cc_start: 0.6590 (mttt) cc_final: 0.6232 (mtpt) REVERT: D 60 LYS cc_start: 0.6616 (mttt) cc_final: 0.6210 (mtpt) REVERT: D 83 GLU cc_start: 0.8513 (mt-10) cc_final: 0.7881 (tp30) REVERT: E 60 LYS cc_start: 0.7154 (mttt) cc_final: 0.6730 (mtpt) REVERT: E 83 GLU cc_start: 0.8611 (mt-10) cc_final: 0.7970 (tp30) REVERT: B 37 VAL cc_start: 0.6936 (OUTLIER) cc_final: 0.6527 (m) REVERT: B 60 LYS cc_start: 0.6553 (mttt) cc_final: 0.6189 (mtpt) REVERT: C 37 VAL cc_start: 0.7236 (OUTLIER) cc_final: 0.6964 (m) REVERT: C 60 LYS cc_start: 0.6671 (mttt) cc_final: 0.6271 (mtpt) REVERT: F 60 LYS cc_start: 0.7234 (mttt) cc_final: 0.6766 (mtpt) REVERT: F 83 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8025 (tp30) outliers start: 20 outliers final: 17 residues processed: 41 average time/residue: 0.0916 time to fit residues: 4.3586 Evaluate side-chains 46 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 26 time to evaluate : 0.096 ------------------------------------------------------------------------------- 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 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 C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU 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: 3.9990 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 0.2980 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.4478 r_free = 0.4478 target = 0.179503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.135550 restraints weight = 2630.749| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.43 r_work: 0.3745 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2507 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= 0.170 Angle : 0.583 4.419 3796 Z= 0.320 Chirality : 0.050 0.128 498 Planarity : 0.002 0.008 450 Dihedral : 13.562 97.935 444 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 7.78 % Allowed : 9.26 % 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: -3.88 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR F 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 0.00374 / 0.17 ( 2788) covalent geometry : angle 0.58317 / 0.32 ( 3796) hydrogen bonds : bond 0.02548 / 1.40 ( 28) hydrogen bonds : angle 7.14284 / 4.59 ( 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 50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 29 time to evaluate : 0.099 Fit side-chains REVERT: A 37 VAL cc_start: 0.6860 (OUTLIER) cc_final: 0.6443 (m) REVERT: A 60 LYS cc_start: 0.6736 (mttt) cc_final: 0.6365 (mtpt) REVERT: D 60 LYS cc_start: 0.6679 (mttt) cc_final: 0.6287 (mtpt) REVERT: D 83 GLU cc_start: 0.8528 (mt-10) cc_final: 0.7889 (tp30) REVERT: E 60 LYS cc_start: 0.7198 (mttt) cc_final: 0.6786 (mtpt) REVERT: E 83 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8000 (tp30) REVERT: B 37 VAL cc_start: 0.7019 (OUTLIER) cc_final: 0.6656 (m) REVERT: B 60 LYS cc_start: 0.6638 (mttt) cc_final: 0.6306 (mtpt) REVERT: C 60 LYS cc_start: 0.6696 (mttt) cc_final: 0.6330 (mtpt) REVERT: F 60 LYS cc_start: 0.7319 (mttt) cc_final: 0.6843 (mtpt) REVERT: F 83 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8045 (tp30) outliers start: 21 outliers final: 19 residues processed: 44 average time/residue: 0.0900 time to fit residues: 4.6256 Evaluate side-chains 50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 29 time to evaluate : 0.101 ------------------------------------------------------------------------------- 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 C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU 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: 6.9990 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.4518 r_free = 0.4518 target = 0.184298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.140197 restraints weight = 2645.138| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 2.39 r_work: 0.3959 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3848 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2788 Z= 0.116 Angle : 0.534 4.371 3796 Z= 0.290 Chirality : 0.050 0.129 498 Planarity : 0.002 0.007 450 Dihedral : 13.330 97.205 444 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 7.78 % Allowed : 10.00 % Favored : 82.22 % 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 : -2.83 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR B 39 PHE 0.011 0.003 PHE B 94 HIS 0.005 0.003 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 2788) covalent geometry : angle 0.53358 / 0.29 ( 3796) hydrogen bonds : bond 0.02351 / 1.29 ( 28) hydrogen bonds : angle 6.97817 / 4.48 ( 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 46 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 25 time to evaluate : 0.100 Fit side-chains REVERT: A 37 VAL cc_start: 0.6878 (OUTLIER) cc_final: 0.6449 (m) REVERT: A 60 LYS cc_start: 0.6880 (mttt) cc_final: 0.6513 (mtpt) REVERT: D 60 LYS cc_start: 0.6765 (mttt) cc_final: 0.6376 (mtpt) REVERT: E 60 LYS cc_start: 0.7324 (mttt) cc_final: 0.6912 (mtpt) REVERT: E 83 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8004 (tp30) REVERT: B 37 VAL cc_start: 0.7050 (OUTLIER) cc_final: 0.6682 (m) REVERT: B 60 LYS cc_start: 0.6845 (mttt) cc_final: 0.6472 (mtpt) REVERT: C 60 LYS cc_start: 0.6880 (mttt) cc_final: 0.6484 (mtpt) REVERT: F 60 LYS cc_start: 0.7401 (mttt) cc_final: 0.6916 (mtpt) REVERT: F 83 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8045 (tp30) outliers start: 21 outliers final: 19 residues processed: 42 average time/residue: 0.0927 time to fit residues: 4.5256 Evaluate side-chains 46 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 25 time to evaluate : 0.100 ------------------------------------------------------------------------------- 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 C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 0.0470 overall best weight: 2.1884 ------------------------------------------------------------------------------- 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 = 0.4495 r_free = 0.4495 target = 0.181798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.137522 restraints weight = 2690.915| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.42 r_work: 0.3754 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2788 Z= 0.156 Angle : 0.565 4.408 3796 Z= 0.310 Chirality : 0.049 0.127 498 Planarity : 0.002 0.007 450 Dihedral : 13.149 95.009 444 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 7.78 % Allowed : 10.00 % Favored : 82.22 % 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: -3.76 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR A 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 0.00345 / 0.16 ( 2788) covalent geometry : angle 0.56493 / 0.31 ( 3796) hydrogen bonds : bond 0.02414 / 1.33 ( 28) hydrogen bonds : angle 7.08973 / 4.55 ( 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 47 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 26 time to evaluate : 0.097 Fit side-chains REVERT: A 37 VAL cc_start: 0.6765 (OUTLIER) cc_final: 0.6352 (m) REVERT: A 60 LYS cc_start: 0.6710 (mttt) cc_final: 0.6336 (mtpt) REVERT: D 60 LYS cc_start: 0.6674 (mttt) cc_final: 0.6270 (mtpt) REVERT: E 60 LYS cc_start: 0.7281 (mttt) cc_final: 0.6874 (mtpt) REVERT: E 83 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8010 (tp30) REVERT: B 37 VAL cc_start: 0.6956 (OUTLIER) cc_final: 0.6584 (m) REVERT: B 60 LYS cc_start: 0.6633 (mttt) cc_final: 0.6268 (mtpt) REVERT: C 60 LYS cc_start: 0.6704 (mttt) cc_final: 0.6296 (mtpt) REVERT: F 60 LYS cc_start: 0.7311 (mttt) cc_final: 0.6837 (mtpt) REVERT: F 83 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8014 (tp30) outliers start: 21 outliers final: 19 residues processed: 43 average time/residue: 0.0880 time to fit residues: 4.4112 Evaluate side-chains 47 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 26 time to evaluate : 0.095 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 6 optimal weight: 0.0000 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 35 optimal weight: 0.0970 chunk 33 optimal weight: 0.7980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.4528 r_free = 0.4528 target = 0.185387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.140864 restraints weight = 2644.054| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.38 r_work: 0.3782 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2788 Z= 0.116 Angle : 0.529 4.276 3796 Z= 0.288 Chirality : 0.049 0.127 498 Planarity : 0.002 0.007 450 Dihedral : 12.914 94.436 444 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 8.15 % Allowed : 9.63 % Favored : 82.22 % 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 : -2.77 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR B 39 PHE 0.012 0.003 PHE B 94 HIS 0.004 0.002 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 2788) covalent geometry : angle 0.52938 / 0.29 ( 3796) hydrogen bonds : bond 0.02316 / 1.27 ( 28) hydrogen bonds : angle 6.93466 / 4.46 ( 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 47 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 25 time to evaluate : 0.057 Fit side-chains REVERT: A 37 VAL cc_start: 0.6716 (OUTLIER) cc_final: 0.6308 (m) REVERT: A 60 LYS cc_start: 0.6562 (mttt) cc_final: 0.6229 (mtpt) REVERT: D 60 LYS cc_start: 0.6602 (mttt) cc_final: 0.6212 (mtpt) REVERT: E 60 LYS cc_start: 0.7211 (mttt) cc_final: 0.6816 (mtpt) REVERT: E 83 GLU cc_start: 0.8607 (mt-10) cc_final: 0.7990 (tp30) REVERT: B 37 VAL cc_start: 0.6881 (OUTLIER) cc_final: 0.6514 (m) REVERT: B 60 LYS cc_start: 0.6536 (mttt) cc_final: 0.6178 (mtpt) REVERT: C 60 LYS cc_start: 0.6639 (mttt) cc_final: 0.6231 (mtpt) REVERT: F 60 LYS cc_start: 0.7245 (mttt) cc_final: 0.6764 (mtpt) REVERT: F 83 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8005 (tp30) outliers start: 22 outliers final: 20 residues processed: 43 average time/residue: 0.0554 time to fit residues: 2.7699 Evaluate side-chains 47 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 25 time to evaluate : 0.055 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 17 optimal weight: 0.0370 chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 4 optimal weight: 0.0060 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.4874 ------------------------------------------------------------------------------- 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 = 0.4607 r_free = 0.4607 target = 0.193558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.148667 restraints weight = 2460.334| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.33 r_work: 0.3892 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3785 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.011 2788 Z= 0.072 Angle : 0.466 3.907 3796 Z= 0.255 Chirality : 0.049 0.129 498 Planarity : 0.002 0.007 450 Dihedral : 12.594 93.421 444 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 5.93 % Allowed : 11.85 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR B 39 PHE 0.008 0.002 PHE A 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00137 / 0.07 ( 2788) covalent geometry : angle 0.46594 / 0.26 ( 3796) hydrogen bonds : bond 0.02017 / 1.13 ( 28) hydrogen bonds : angle 6.61672 / 4.26 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 979.51 seconds wall clock time: 17 minutes 32.03 seconds (1052.03 seconds total)